How do we feel about Omega?

Spoilers Voyager Season 4.

I know that the Federation/Star Fleet tries to keep>! from overstepping and acting as arbiters of the universe, except in this one very specific instance. Justifying it as "we are keeping people from making a galaxy-ending phenomenon" is one thing, but it could also be viewed as "we like warp, this destroys warp capability, lets impede anyone trying to destroy our warp capability" which is kind of nasty, especially the fact that "the prime directive is rescinded" for this directive. Polaric Energy from an earlier episode seems just as messed up, yet they aren't making decisions on that.!<