The theory in the newsarama article makes a lot of sense. Even if it isn't completely right, I believe it's closer to the truth than all the other theories.
I can even imagine what the reveal will be:
John Harrison: No, Kirk....Khan is my great..great... grandfather!!!
Captain Kirk: Nooooooo!!!!
:"Kirk, you can destroy the Emperor, he has forseen this. It is your destiny, join me and together we will rule the galaxy..."
oh wait, wrong franchises.