The genocidal attack on the Founders was explicitly a Section 31 action, and some characters equally explicitly verbally condemned Section 31. On the other hand, Section 31 was given impossible powers of subversion. The justification of such regimes always starts with the implicit claim that if "we" do what is necessary, then "we" can be safe. The unspoken assumption that various sorts of villainy are needed, in the sense of really having the power to make us safe, is not only left unexamined. It is thrust upon the viewer by fictionally giving Section 31 the power it claims. Thus the only possible choice within this thought paralyzing assumption is, is it better to be a live villain or a pure dead man? That for most of us is a no brainer. It's a way of loading the (moral) question. Bad writing, and bad morality too.
No one knows what the Prime Directive really means. In Star Trek, it meant things like Patterns of Force were criminal, no matter how well intentioned they supposedly were. The interpretations advanced by some characters, sometimes, in modern Trek, don't even make it clear how it is possible to trade with or even talk to other aliens without accepting their professed values without any criticism. This is just stupidity.
The notion that the Federation cannot give conditions for membership is that same as saying that the Federation central government cannot pass laws binding upon the membership. This is equally stupid. The absurd implication that a caste system would be in Bajor's interest shows, I think, that some people's motive for denigrating the Federation is a general detestation of old fashioned notions of democracy and humanitarianism in general left over from Star Trek. The connection is clearest in the Voyager episode Unity, where a mental democracy is portrayed as the origin of the Borg.
But, rest happy: The rebooted movie series has no moral content whatsoever.