Doubt it's going to happen - I prefer the alternate timeline thing, because it allows JJ to tell a story without actually stepping on Trek (unlike G Lucas re-writting stuff, we had Enterprise which was bad enough).
For me it wasn't Scotty's beaming that I thought was the issue, but that he beamed inside a waterpark in the engineering room - that whole scene made my stomach turn. Not due to the shaky cam, but why the hell was it there in the first place? The replicators have long been held to re-purpose matter due to the lack of available materials in space and the sonic showers were used so large amounts of water, which is both heavy and finite, would not be needed. So that whole section was off putting. For me, I like that in the 2nd movie Khan isn't dead per se; THAT equals sequel fodder and a chance to do something totally original.