Barry didnt do any of that. It was Reverse Flash;
Reverse Flash "Here we go, things are back to how they should be. Well for me anyway. For you well, I guess you will just have to wait and find out. "
Clearly Reverse Flash is responsible for Cisco Brother being killed and many other things.
Even if that is true, no one thinks that Thawn is still trying to game the system, and it wouldn't have been posible without Barry waving a big ass green flag giving him permission to jigger with time.