I'd point out that...
A: we didn't actually see a single Raider or Viper spaceside. (Nor have Vipers ever proved particularly adept at missile interception, though granted they're too busy fighting for their lives normally.)
B: whatever crew problems he had were not hindering Pegasus' rate of fire noticibly. (They might have contributed to damage control problems, but this is again dependant on going straight in and absorbing fire, which may not have been necessary.)
C: He jumped in and found himself at the very least just outside engagement range. Pegasus was in the fight before the Cylons were able to deploy to cope with it.
D: The Cylons reacted to Pegasus' arrival by a temporary withdrawal; they ceased firing on Galactica when they realized there was a second battlestar in the area. This is entirely logical, since Galactica was pretty much dead in space and would be there when they got done with Pegasus.
E: What exactly it takes to bring back a basestar is probably different from what it takes to bring back a humanoid model; there are observations about resources made above that argue against them being willing to lose the basestars; Cylons (aside from humanoid Cylons) have never been particularly suicidal. Even the humanoid ones don't
like dying (witness Cavil's comment on it), and they have retreated despite the presence of resurrection facilities before (Hand of God).
F: Most damning, the basestars had to know that the contingency plan for this occurance involved detonating the nuke on New Caprica, which would wipe out those planet-based facilities. (That the plan would not be carried out was not clear until they had Pegasus against the ropes.)
EDIT: I also have to question why Lee was all "OMG no!" about sending in both Battlestars. We know that the plan involved Galactica holding off at least a few while the civvies escaped, and Adama did not seem particularly worried about having to deal with two. It was when the other two jumped in that things went to hell. If Pegasus had gone along originally there is a real possiblity they could have defeated or at least rendered unable to fight the two that jumped into orbit before the two from the nebula had been able to get into the battle; it would have been a pair of 2v2 matchups instead of a 4v1 and 3v1.
Either way, booting him back to a fighter cockpit seems kinda lenient, but I suppose they don't have pilots to waste.
