Hmm, that does sound annoying having it not matching the levels properly. Isn't there some kind of option to toggle that? I'm not much of a PvE'er so i'm not really sure.

When it came to blowing up the comet. I just went for it and nothing else blowing up all the fragments and everything without hassling the enemy ships that were growing rather rapidly around me.
T^hankfully though i was in a carrier and could soak up the fire from them without too much bother. It was only right on the last couple of pieces of the comet that i really started getting hammered and i popped about 3 seconds after the final piece had been destroyed.

Retrospectivly i probably really shouldn't have done it this way at all. but ah well it worked.