As an evil guy I helpedthe ghouls attack the Tower and I killed all the ghouls as well and I wasn't allowed back in my apartment (which I already had) becuase it said something like "It isn't safe"

Is this a glitch every time I try it (and I've started the game about four times) it's always the same thing?

I know your not allowed into your room during the quest but you should get in 24 hours(in-game)after the quest is completed, you may have to re-load an old save.

Try reading the wiki article about it :read: http://fallout.wikia.com/wiki/Tenpenny_Tower_(quest)

Forget about the Tower for a while. Go do a another side quest or something. Then the next time you come back. Everything should be fine.