First off, would be repair the game install, second is a question, you have cleared the bunkers for all three regions correct?? You technically can kill the heralds, but not clear their bunkers on two of them, meaning you don't get the next step. There should be no one at the compound until you get close to the church doors, and then it plays a cutscene.
Unless you are wanting to go NG+ then in some ways, celebrate the fact you don't have to go through the dog poo ending.......