I didn't get the impression that they were trying to paint the Federation as ultimately evil, but rather show the reality of "peace". You could likewise argue that the Federation itself was a social justice machine, absorbing planets into its ranks and forcing political correctness and tolerance in the pursuit of its own idealist vision of peace. The showrunner, Ira Behr, has said he wanted to portray the Federation with the concept that everyone and everything exists as a shade of grey, without pointing and saying these are the good guys and these are the bad guys. For example, Major Kira was a hero on Bajor, but her actions to help her people directly and indirectly resulted in the deaths of thousands of arguably innocent Cardassian civilians and so she was seen as a terrorist by the Cardassian goverment. She had no regrets for what she did (as she felt she did what she had to do to free her people from Cardassia's occupation), and the show never forced her character to repent or overtly justify herself, but she was forced to come face to face with her past on occasion and she is a classic example of DS9's use of the moral grey area. DS9 prided itself on creating character-driven stories, as opposed to TNG's story-driven characters, so I feel like this is a natural next-step in that process, seeing as the Federation as an ever present concept is a character in itself.
Edit: I'm currently watching S3,Ep15 of DS9 right now, and Odo has a line that I think sums up the above pretty well:
"I'm not suggesting anything, but it's been my experience that all humanoids have an agenda of some sort, and their agendas can influence them without them realising it."