Wow folks!! I've been out of town and a lot has happened!
How is Faith doing? From my experience spaying and neuturing goes a long way to calm animals down and make them less territorial and more affectionate to their human friends. Please don't give up on her too soon. There was a good suggestion that you keep Faith and Thomas separated and that is a good one even though it is inconvenient. Once they are BOTH neutered and recovered I'd try and put them back together and depending on each bunnies personality they may fall in love right away or it may take a few days. Buns are extremely territorial, you might re-read the House Rabbit Society's link on introducing bunnies.

With regards to neutering/spaying and health care - not that you asked, but I have to say it anyways, if you don't have a rabbit specialist vet please try to find one. I've heard horror stories about well-meaning but "unknowledgable-about-rabbits" vets that would make your hair curl. Buns have lousey immune systems and sooner or later most buns will require expert care.....I'll get off my soap box now.
Please let us know how Faith and Thomas are doing.