I do not thinking killing Enemies have to do any thing with bad ending ....
I think You should help/let them go who have surrender to get the good ending & all of them should be rightfully done. For example
Pulling the liver in the Nazis prison camp In the upper guard room to let go the Prisoner The green light shine over the cages, Letting go the Nazis solider who was picked by his fellow soldiers go & u find him crying in the freezer. Letting go to the Nazis Solider who surrenders When you caught him reading a book & letting go the Nazis guard who surrenders when you & friend (Forgot the name)
escape to a rail kart ... This is my second play thought Except these i have nailed almost all of them ...