I still don't get what this issue is. I can't find anything in the rules or roles stating the killer's hit takes precendence over the godfather's.
Personally, when I host, the way I view hits are as such, if the killer or godfather is voted out or there is a role that allows them to be killed in the day, then they don't get a hit at night. But if they survive the day, then all night actions go through. So, if they target each other, they both die. I try to keep it simple like that.
Now, the simplest way to run the game is all hits always go through even if that person is killed during the day. Sure it might screw one or two people out of a victory but you won't run into this problem as well. That said, I prefer to give people the bonus of avoiding a hit by a good vote out.