I came across this box set and it's really messing me up for a lot of reasons (it is marked TOS despite having characters from all over the place, and for some mistaken reason Gul Dukat is included) but what I really wanted to talk about was Q's inclusion.
Do people usually consider him a villain?
I suppose he has done a lot of things that would be considered antagonistic, with a big one getting a number of Enterprise crew members killed in the first encounter with the Borg, but that seems, at least from his point of view a tough love moment. In the long term, Q did seem to have the survival of humanity as a goal. His judgment of humans was pompous but not villainous.
Does that make the Federation villains because of the Prime Directive?
If they have Omnipotence and know the future, yes. I understand their prime directive but don't agree with it but I wouldn't call them villains. More of a bureaucratic issue to prevent meddling in other civilisations. I think in real life the federation would try to help everyone and get them to join the federation and take some of their resources to fight the Borg and others that are against them.
To be omnipotent and knowing the future don't make you know better than others to separate good from evil. Is it right to save a civilization if to do that you have to destroy an other?
You would have to keep helping so the 1st civilization does not stomp out the 2nd.