You could make a moral arguement about the merits of both sides, which is what made it such a compelling story arc. These weren't your generic bad guys of the week. Sure they were the antagonists, but you can't help but sympathize with them and the poor situation they were dealt.
As for your question, me personally? If I lived in those colonies, I probably would join up. Otherwise if I lived elsewhere in the Federation, I'd probably speak up for them sympatheticly, but draw the line there. Definitely wouldn't pull an Eddington.