Or why not just allow ships to repair themselves? In SFC you could pack repair kits and they could be used to repair certain parts of the ship.
Though in SFC you could target certain areas for your weapons/marines to destroy.
Naturally the resources were limited and thus you would equally run out of repair kits sooner or later, but you did have certain tactical possibilities.
Also, it could be possible to repair some number, say 10% of your ship, without resources. This could represent some jerry-rigging from Scotty/McGuyver. Just enough to bring some systems back online, but the next critical will break it permanently.
@Flare:
I used to do similar in SFC as well. When timed correctly at the right speed, you could have two waves of drones on top of each other. Then you move all energy towards forward shields and overloaded torpedoes and your little Miranda class could take out a Klingon dreadnought.
The AI should recognize that tactic and run-baby-run, whiles dropping mines (a good addition for SF btw).