In my opinion it is what it is.. Personally I was annoyed with naive Starfleet officers like Julian freaking Bashir who want to cling to morality at expense of survival. Bottom line is this, the Federation IS no different than any other race when it comes to survival. If it is between morality and survival, Survival will and should always win. We saw it in In the Pale Moonlight - no Romulans = Federation loss. Saw it in Extreme Measures - Genocidal Founder Killing disease? The Federation was on the verge of collapse. Ransom and his aliens in Equinox.. yes his justification was completely wrong morally, but in the case of survival seemed like the best option at the time.
Bashir said once "so what we are saying is that we are no different than our enemies? That we forget our principles blah blah blah..." Yes, Dr., because if we clung to the rules of war and morality there would BE no Federation. It would have been conquered centuries ago. I am glad DS9 devoted entire episodes to this dynamic because it really irks me personally (I REALLY REALLY dont like Bashir).