The fact originally conceived villain John Harrison turned out to be Khan in a contrived twist, was incidental to the storyline and amounted to a gimmick.
And it makes no sense to me at all that they went to him for help designing the Vengeance
. You would go to your 23rd century engineers for that, not Khan.
I read a Lindelof interview that more or less explained why it ended up being Khan. Basically they were hearing "don't do Khan" so much that they felt they had to do Khan. Brer Rabbit was even namedropped.
And now that Khan's out of the way... wait for it... it frees them up to do something original. Because that worked out so well last time.
You know, sometimes when people are incessantly telling you that you shouldn't do something, it's better to actually not do the thing everyone is saying you shouldn't do.