I ran a campaign several years ago, before HG came out. I didn't use any grander mechanics than the Core Rulebook.
As the Referee, I decided how the overall battle was going to go. If I needed to, I rolled a couple of dice to give me an indication of who was lucky.
All of the PCs were on a single Cruiser. So I let them roll for attacks and rolled attacks against their ship. It gave the atmosphere I needed, and let the PCs affect the overall outcome - if their Cruiser easily defeated their enemy due to great actions by the characters, I gave them a better chance of winning.
I used this technique twice - once the PC's were very heroic and defeated their enemy, but the battle was lost and they had to fleet. In the second one, their actions turned the course of the battle, and their side won.
If you make it about the PCs, not the War, then you don't need a lot of special rules. Make some decisions and then have the PCs play through the action. No PC group is going to be important enough to affect an entire interstellar war, or even a single battle with Trillion Credit Squadrons attacking each other - BUT, they can and should affect a single combat within that overall battle, which could ripple across the war.
They could have the only winning battle in a losing war ala Sheridan in Babylon 5, or they could be the only ones to lose a battle in an overall route of the enemy, or anything in between.