If they had a great story that focused on Mitchell, they would use Mitchell regardless of the comics. And the comics are not canon.
That would make sense if the comics had come out before the movie was written, but as Orci is involved in writing both and they have said a couple of times it is supposed to fill in some of the time before the two movies its unlikely he would use the same villan twice.
That is unless Mitchell undergoes some sort of Time Lord style Regeneration too.
Well, that alternate universe story isn't thought through. Any sort of big villain would almost certainly have operated in the Prime universe as well.
Possibly, but as Spock said in the first movie a new timeline means a completely new chain of events, this would mean that what happens to Harrison in this timeline may not have happened in the original one meaning he did not turn bad...we wont know until the film and we learn those motives the Cumberbatch talked about.