Keep a good relationship with her dad and family if at all possible. Don't allow her to make it awkward and try not to put them in an awkward position either. If you still might want to fix your marriage, it will not help if she convinces them you are the problem and she has played no part in this. They could be in support of MC so that you can work towards keeping an intact family for the kids.
So yes, friend her dad back. He will take it as a snub if you don't and it will inflame the situation. If it goes all the way to divorce court and beyond, you can unfriend him two years from now if you want.