They didn't really get shafted, atleast not with their fates, story wise. Magik stuck some avengers in hell, basically. Colossus beat Spider-Man until his blood splattered on Collossus's face. Emma either really injured or killed a guy for lying about something, and had half the mutants on utopia worshiping her. They also all took over the earth. The avengers didn't make them do that, and for about 75% of the time, the Phoenix didn't make them do it, either. They should be wanted criminals.
Now, the writers may have screwed them (although I honeslty think something like this has been building since House of M), but at this point, just from an in universe perspective, the 5 phoenix mutants should just get locked up. I'm also not too sure about rachel needing to be involved more than she was. I don't think she can really be counted as the same kind of Phoenix. She obviously didn't have the full, pretty sentient, Phoenix Force, or she would have gone crazy, like every phoenix host (not just on earth) has. She had a weaker version, or just one without the mind altering properties, but she was not dealing with the same creature/force of nature that was in AvX. I don't think her will to resist the destructive impulses of the real phoenix would be stronger than Jean Grey's, the 5 or Hope's, so I would just assume that her version was different, and that she would have turned just as evil if she had been effected by it (although she would have been better initally, I doubt she would have stuck anyone in hell/limbo on earth).