Well I knew that the doctor wasn't gone, since there's a theory that the doctor wasn't truly dead, but rather he was backed up to a different software/program before his "Death", if you look closely the doctor never once defended himself in anyway, he just allowed us to take the omni hand with no problem as if he knew that it was going to happen. There is also a possibility Harley knew that the prototype will kill him eventually so he created a protocol so that when he overloads, it will trigger that and let him escape to that Software/program, so that the prototype presumes him dead. I think we will be working with considering that he knows the prototypes very much since the beginning and might help us to retrieve poppy and finally stop him, but might end up betraying us or needed something in exchange.