Beyond the issue of religion, Roddenberry, etc. developed Khan as a character who was non-white. Now Abrams, etc. has made him white, with no explanation as of yet. I think at the least an explanation should've been given in the film.
As a person of color I was disappointed that they went that route. To be fair, they were looking at Benecio Del Toro (sp), but I wish they had looked at other non-white actors, particularly Indian actors. Granted this might have forced them to give up the ghost on Harrison's secret identity, which was a big deal for them, but still I think it would've been better than whitewashing the role.
At the end of the day it means, to me, that one less role (and in a major film) goes to a person of color and I don't think that's a good thing for Hollywood or audiences down the line.
Before people think I'm downing Abrams I do think he has been pretty good on the diversity front, compared to most in Hollywood. I like what he did with Alias and Undercovers.
In his Star Trek, Uhura has taken on an importance that she never had in the original series and within Star Trek period black female characters haven't gotten much attention or development at all (possible exceptions Lily Sloan and Kasidy Yates). All that being said, Uhura still is too much of Spock's girlfriend, but at least she gets more face time and is in the mix more than Nichelle Nichols was allowed to be (Nichelle is still my favorite Uhura though). At we got some short but sweet scenes with Sulu in both Trek '09 and Into Darkness. So, I think Abrams gets it to some extent and that's why the decision to whiten Khan is even more disappointing to me.