Another idea to measure the success of a mission is to look at Heroes of Battle, a supplement for Dungeons and Dragons 3.5 Edition. That book gives rules ideas for a the small-unit tactics of D&D to be applied to large-scale battles.
But there are more important things to large-scale combat than the growth and progress of a small band of special forces (i.e. the players' party). So while XP is calculated normally, a system of measurement within the army they work for is needed, not only to determine how well the battle as a whole went, but how well the player characters did, and how well-regarded they are. (Ranks can be handle in an ad hoc manner, as needed by the story, but other things are useable.) There are Victory Points and Recognition Points. Victory Points represent how well the battle has gone. Certain actions are worth a certain number of Victory Points; killing individual soldiers isn't worth any, but cutting down bridges across a chasm to cut off ground-based reinforcements might be worth 100 points; firing enemy siege machines might be worth 250; taking a critical cliffside might be worth 500; and so on. Victory might be achieved if 1000 Victory Points are acquired. If rather more than that are acquired, a massive rout is achieved; if somewhat less are scored, an acceptable victory; if less than that, a draw; less than that, a recoverable loss; less than that, a crushing defeat.
Recognition Points are different; these are for exceptional and often public displays. There are a number of examples given in the book, including capturing an enemy standard (battle-flag). The more notorious the unit whose standard you capture and hold, the more Recognition Points you earn.
Destroying a notable unit, similarly, would also earn recognition points; if a particular unit has a reputation for being unusual compared to similar ones--if the Fifth Elite Stormtroopers had the fanatical attitude of your average unit of Soldiers, for example--they might simply be more famous, though not any better, and killing them would be more of a blow to morale. In modern warfare this could be expanded into assassination of renowned figures, prevailing in aerial dogfights against legendary aces, blowing up a world-famous landmark, or even taking a celebrity hostage.
Rescuing an endangered unit is rarely seen as a bad thing--if you save soldiers while not endangering a mission, you not only kill your share of the enemy, but your new friends' share as well, keep more of the army intact, and in general keep the position of your side strong.
Simply surviving overwhelming odds is an impressive feat. If done properly, it marks you out as being one of the physically and mentally toughest people on your side (even if it was just luck or happenstance). But aside from that, surviving overwhelming odds means you killed far more than your share, lost the battle, and still kept going--it means you did all you could be expected to do and then some and still weren't victorious, so who could have been? That a loss was inevitable is small comfort, but may still be comfort enough. This is of course to say nothing of surviving overwhelming odds and prevailing...
Each of these acts, in D&D, has a formula for calculating recognition points earned. Sometimes an act will not score many (or any!) victory points, but will grant a pile of recognition points. This is for obvious reasons--it's the difference between reputation and reality. In any case, recognition points, unlike victory points (which are simply used to keep score of who won), can be "spent"--to buck for promotion, to receive a decoration, receive special status, and so on.
Similar concepts have already been tried video games. In the X-Wing games, for example, your score determines your rank (though your rank doesn't have much effect on the game as a whole). In addition, your kills determine your rating (from Uncertified to Certified to Expert to Marksman to Ace--you can go higher, to Top Ace to Jedi to Jedi Master, but only through multiplayer), and your bonus points determine your Kalidor Crescent, a medallion given for exceptional bravery and skill to Rebel pilots--every time you score 1000 or more bonus points on a mission, you get the Kalimdor Crescent (or an upgrade--Bronze Cluster, Silver Talons, Silver Scimitar, Golden Sun, Diamond Eyes, in that order).
Now, the use of victory points would be too abstract an approach to Crusader, as victory conditions would be pretty clearly defined. However, here the term "winning the battle, losing the war" comes into play--or, given the scale of conflict, "winning the skirmish, losing the battle". If you rush through and accomplish just your minimum necessary goals, you might do well--but your allies, part of a three-pronged strike mission, might run into more security than they can handle, and their two critical part of the mission outweigh your one critical part; the mission is a win for you and the story advances, but a loss for the Resistance and you have to fall back. So say that "marginal victory" is 500 points, and completing your part of the mission gives you 500 points. However, "worthwhile victory" is 750, and taking out a squad of Vetrons heading out after Shepherd's group, as opposed to sneaking past, is 250--the total is 750, and the Resistance scored a real, workable victory. Meanwhile, Brooks was unable to get past security at her target and her team had to turn back. If you were to shut down power to the whole facility long enough for her to get in and then turn it back on so you could (e.g.) use the computer you need to steal files from, that's another 250, and your total is 1000, a complete victory, and the Resistance advances handily. In each case, though for this descrpition there was only one way to accomplish the main mission, the mission afterwards would be different--if you accomplished one out of three goals, you would have to help the Resistance in their attempts to secure losses while they figure out how to use what you did; two out of three, how to make the most of both of them while minimizing the downside of the third; for all three, how to best take it to the suddenly cut off and surprised WEC forces in the sector. And if you didn't do any, say the computer was destroyed in the final firefight and you didn't do a thing to help Shepherd or Brooks well, it might not have to be a game over...
As for other types of points, the Silencer is already pretty much as deadly as he's gonna be (pretty much...); the Resistance doesn't seem to be the type to give physical medals; and his rank of Captain seems just about right for what he needs to do. However, there are other things granted from achievement.
The modern US military operates on a philosophy of "overwhelming firepower supported by overwhelming logistics". That is, for every combat soldier, there could be hundreds or even thousands of people cooking food, doing laundry, shipping fuel, making bullets, sewing uniforms, repairing vehicles, etc. Logistics is how to make an army able to sustain its fighting force and get it to where it needs to be. And the Resistance tries, but its logistics aren't that great.
It's critically short on many kinds of equipment, so such things have to be rationed. A level of trust is necessary. So rather than a mercantile system of buying weapons and ammo directly, excellent performance could result in more "requisition points", allowing the Silencer to check out more equipment, ammunition, etc. Now, ammunition of course is expended, but the weapons themselves are "on loan" from the Resistance; this creates an interesting game of resource management. You are of course given requisition points at the beginning of most new missions, in order to pick out what equipment you think you'll need; but at the end of the mission, you have to return it. The mercantile system could also be kept, and the Silencer could use money from corpses or pay even Rebels would receive (at least on paper) to buy things from Weasel (or other third-party dealer) to get weapons he'd really own. To really mix it up, the Silencer could also pay the quartermaster money to buy ammo or "rent" weapons; the ammo would be more expensive than it would be coming from the arms dealer, and renting weapons mission after mission would eventually be more expensive than buying the weapon outright, but it's an alternative if you're low on requisition points. Similarly, if you're low on money, you could use requisition points on Weasel, though they wouldn't go as far--this would represent your ability to get the quartermaster to purchase certain weapons the Resistance doesn't have for you, due to his trust for you or your intrinsic authority. The inverse also works: you can sell ammo or weapons (finally) and get money or requisition points, though you can't get requisition poitns from Weasel or money from the quartermaster. Though you should be careful if you sell a piece of equipment you've only requsitioned or rented...
Meanwhile, I've always liked the idea of getting rewards for finding secret shit in games, whether it's better equipment or an increase in a character's actual power (i.e. experience points or new abilities) or more gameplay (i.e. secret missions) or even just a special title marking you as a badass player who found all this awesome shit. The important thing is to scale it; you don't have to find every secret, but the more you find, the better.
One method of putting secrets in would be the "secondary goal". The quartermaster might be running low on ammo, because Weasel's supply lines have dried up. So he asks the Silencer to see if he can do anything on the next mission--not bring pack a pack full of magazines, because even that wouldn't be anything more than a bandage, but look around and see if another supply can be located. Lo and behold, he might be able to discover the location of an ammo dump that can be raided by the Resistance (which could be a secret mission)--or even divert a convoy to a low-security area where Weasel's operatives will be able to raid it. In the former case, the reward might be the secret mission and the chance ot pick up a lot of special ammo; in the latter, the quartermaster would be very grateful, and the character could get a big bonus of requisition points, or even be given a weapon of choice from the supply room.
Other rewards would be more obvious--the discovery of an advanced weapon in the early game (such as the Reaper you can get in mission 2, I think it was, of No Regret), a shortcut to the endpoint of the mission (whether a physical or metaphorical shortcut), a hidden joke (everyone loves monkeys!), or virtually anything else where you get something immediately for doing finding a secret door or blowing a hole in a specific wall.