You know, I wonder if the statements that were made about the "villain" being a character from TOS season 1 were not in reference to the Cumberbatch character but rather to the Peter Weller character. Maybe he is one of the admirals who occasionally appeared on-screen to deliver orders to Kirk and the Enterprise or someone similar. The statements would then technically still be correct.
Supposedly, Weller was new to canon
. But Orci also said that Cumberbatch was from canon, so we'll have to see how that goes.