As a Fed character you can 'kill' every Klingon ship that comes at you, they all stop at disabled when you beat on them enough. The only one you have to be careful with is B'Vat, who WILL try to hit you with ramming speed and will kill himself in the process if he hits you or anything else. The best thing to do with him is to disable him away from everyone else so that he doesn't have a chance to successfully suicide himself. I actually beat it the first time I played it without firing on any of the cruisers. This though was before they changed the way that the cruisers spawn after they kill you, and I totally deathspammed my way through it the first time
The other thing you can do is damage all the comet shards down to just a few percentage points before destroying them. Then, once they are all in such a weakened state, so to speak, you can do a pass and blow them all up quickly before B'vat gets far trying to ram you or the other Klingon ships get close enough to do any damage.