I wouldn't go so far as to say the Alpha Quadrant powers deserved the deaths that came to them--I mean, that's the same as suggesting the Cardassians deserved to have billions of their people killed because of what their governments did.
We rarely got to see a credible dissent within the Federation, either. Most of the time, the dissenters were shown as loony or violent. (Alixis, Eddington, Cartwright, Section 31, need I continue?) To see someone fundamentally disagree with Federation policy and be taken seriously as a character--that's not something I think I ever saw. You never saw a conservative that was treated as anything but a stumbling block, a blockhead, or an enemy: kind of the Cardassian problem in inverse. And THAT is pretty chilling considering the Federation was supposed to be a democracy.