Another thing came to mind that has stuck with me from this novel. When the Enterprise is dispached to pick up the Cardassian negotiator, Akaar says something like. "She's a democrat, our kind of Cardassian."
This rubbed me the wrong way. The UFP is a democracy (more accurately a Republic) but it has allies that are not democracies. For example, the Klingons have been allies for a long time and they have a type of Oligarchy government. Akaar himself comes from a planet that, last we saw, was not a democracy. Then you have the Romulans, which have a Republican goverment but are historically at odds with the UFP. So should the negotiator being a democrat matter? Was this a statement of partiality?
I think it was more an acknowledgement that Cardassians have, politically, been trouble for much of the time the Federation has known them, and that the political movement on Cardassia that finally put an end to that and accepted the Federation's friendship was the democrat movement. Akaar was, as I read it, simply saying "yes, I know Cardassians can be trouble, but this Cardassian's record is of involvement with the social/ideological/political platform that's compatible with our methods and our way of doing things, and so you can be reassured a little, in that she probably doesn't have an agenda that might work against us, or that she'll be resentful of us". I don't think any sweeping judgement was being made regarding how the Federation interacts with alien powers in general; I think it was tailored quite specifically to the situation in the Union.
That said, the Federation may have a non-interference policy, but of course they still have preferences and outcomes they're rooting for. A sense that the Reunion Party and its ilk are the "good Cardassians" and the Directorate, etc, the "bad ones" is indeed going to be present, I'd expect. The Federation wants the democrats in power on Cardassia, not the militarists.