Where did it say the enclave will be evil or vice versa for the bos .And you can kill the bos twice once with the fev then you can bomb the citadel.
Uh...you are force to join the BoS...and you can't join the Enclave? The Enclave, even if you decide to poisen the purifier, will still shoot you on sight (except for that random encounter). You can't even continue the Main Quest without the help of the Brotherhood. Hell, without your approval you are inducted as a Knight for Christ sake! As much as I love FO3 to death I have to be honest about its shortcomings.
Yes, you can bomb the Citadel but it really doesn't affect much of anything. Once again, there are no consequences to your actions. The BoS will just haunt you down, like the Enclave, the end.