Todd Anderson has a nice article about the situation in SCG. I don't agree with everything but I agree with a lot of it.www.starcitygames.com/magic/modern/22722...
Personally I would prefer to just do unbannings for now without necessarily banning anything else.
Although I'm extremely certain that Mystic is safe and should be unbanned, I wouldn't mind letting it stay banned for a while longer, on the other hand Bitterblossom is probably even safer to unban and Todd didn't list it.
Cloudpost should be able to stay for a while longer, I'm not so sure if all the rituals should stay but I wonder if the best option is to go for Ponder or Preordain even (as that goes for all the combos including Splinter Twin / Blazing Shoal, whereas banning Rite of Flame doesn't). Peer is probably stronger in most combos than Ponder / Preordain, but doesn't "manipulate" creatures or lands, so perhaps it wouldn't be the right choice.
I'm very certain that Inkmoth Nexus can stay unbanned if the consistency is toned down as well.
Emrakul may eventually need to go because it is impervious to most realistic answers that would deal with more typical "reanimator" targets and it usually just wins in a single swing (unlike, say, Progenitus which is also impervious and hits hard - but not as hard - and if it is used with Goryo Vengeance / Through the Breach won't leave the opponent without permanents).