I do wonder how long before a prime universe reference to John Harrison occurs.
How in the world could there be a Prime Universe reference to an alias that Khan was only assigned after he was awakened in an alternate timeline?
Well, consider Good That Men Do
which is an entire novel dedicated to saying "That episode no one really liked? Well, turns out it was a dodgy holorecording. This is what ACTUALLY happened." You could have a writer come along who didn't like Into Darkness
and drop the name into dialogue in the prime universe that makes the identity questionable.
I'd rather not hover toward any story elements, but a knowing nod could also take place. List of known aliases on a computer screen, list of cover identities, etc. etc.
(My brain is also wired to comics where codenames used by characters from alternate timelines filter back to the main one.)