I am well and thoroughly spoilered with this film - i haven't seen it yet - and here is my feeling about Khan...
First of all, I was hugely making a case for Cumberbatch playing practically anyone but Khan. I hated the idea of bringing Khan back and the idea of a white, British Khan even more.
Now I am intrigued and excited and feel that the writers may be doing for this character what Nolan did with the Joker in "The Dark Knight" - a thorough deconstruction, and written as Khan would be written *now* (and it would also not be cool presently to show an Indian or Middle Eastern guy as a terrorist type; going with the original casting choices or a white guy may be safer... but in the end, NOBODY here is going to be pleased). Something that to me had always been scrimped on in TOS, was that we never before really saw that much of Khan's "superiority". Also, there were aspects of that characterization and that story that suffered from being "15 minutes in the future" so that now they're horribly dated. And people prefer more complex and nuanced villains now.
If you consider JJ's "Star Trek" to be adding to an existing body of work based upon a mythology rather than attempting to be a direct remake of TOS or the films, and consider this new body of work to be updating based upon current sensibilities, it makes sense.
Comics and the like have a long history of reinterpretations and multiverses - I kind of think of JJ-Trek as the Trek version of Marvel's "Ultimate" universe.
Plus, Khan was definitely out there and they may have needed to get him out of the way to move on and tell new stories.