The Doc always becomes hostile after talking to him, unless you pay to be healed. Probably this mechanic kicks in when you load.
As nobody in the house is of importance to the main story, you can kill them, but lose some karma.
Maybe you can manage to talk to your companion, and dismiss him before the fight starts, so that you're able to flee the scene. Come back to pick your buddy up (maybe after a day rest) and see if the situation is calmed down again.

Although the easiest way would be to fall back to an older savegame. By the way, make sure to have plenty of them, because the game is famous for corrupting saves, so be prepared.