I'm not entirely sure he doesn't. It's just speculation, but in that scene between Xavier and Cykes, it really seemed to me like the Professor was hiding something. He's a smart guy, and he has big, BIG plans for the future of mutantkind that we don't yet know the extent of. I think by now, Xavier might have been able to piece together a rational reason for why and how Cable came about, and he's already looking for a way to terminate him without showing his own cards.
I'm not willing to bet on it, but I certainly wouldn't put it past Kirkman.