I see Kira at the beginning as somebody who sees the Federation as another occupying force. So it's not be hostile toward everyone, it's directed at the Federation and Cardassia. In her mind at the beginning of the episode, all large foreign powers are the same. It's through her interaction with humans in the first season that she really learns the Federation isn't going to do anything to Bajor against Bajor's will or make them into a puppet state.
I do think TNG and DS9 are very similar series, or at least more similar to each other than any other two Trek series. TNG's more optimistic and idealized, DS9's more socially realistic, but the two shows have pretty much the same story logic.