It would take a fairly drastic power-up on Seidou's part to contend with present Kaneki, since Haise was nowhere near this skilled when they fought before. I'd put my money on Amon doing real damage to Ken, though. He managed to escape Aogiri, then turn around and hunt them without much effective resistance. They seem to really want him dead, which suggests they take him seriously, unlike Seidou who they treat like a pet.