The fact that there's an in-universe explanation for why Khan became a white guy in Into Darkness does not make the decision to cast a white guy to play a Sikh role any less offensive.
No one wonders if real world Sikhs were offended when Montalbán--a son of Spanish immigrants to Mexico--was cast as Khan back in 1967.
Nope! "The Alternate Factor" was crap
Plotting problems aside, the Lt. Charlene Masters character was a standout in that story and should have appeared in more episodes.
I mean, for many years Paramount did not consider TAS to be canon. Now they do.
Originally, it was considered canon, given the seal of approval (as an official continuation of TOS) by Fontana and Roddenberry at conventions predating TAS' premiere. It was Roddenberry himself who decided to "de-canon-ize" TAS many years later, a decision Paramount did not reject...until TAS references were added to Berman-era series.
That is a valid artistic goal, but it is not universally true. There are plenty of stories where breaking continuity was the right decision to make. For instance: Is the depiction of Gallifrey and the Time Lord military high command on the last day of the Time War in the Doctor Who 50th anniversary special "The Day of the Doctor" really consistent with the depiction of Gallifrey, the Lord President, and the High Council in "The End of Time, Part Two?" No, it's not. There's an attempt at a brief handwave, but realistically the two depictions contradict one another. But fuck it: "The Day of the Doctor" is an amazing story that requires contradicting part of "The End of Time, Part Two" to work, so as far as I'm concerned the writer made the correct decision in breaking continuity.
The issue is that the story which broke continuity still has the original sitting next to it forever--with the former always standing out as making what some would describe as an unnecessary change which created contradictions in a particular story, arc or character where none existed before. A similar case is ST's Zefram Cochrane and the flat out upending of the original (and sympathetic) character from TOS'
Metamorphosis", transforming him into the drunk, aging hippie caricature from
Star Trek: First Contact, with Brannon Braga admitting he (and his co-writers) created an entirely new character, thus, there's no way viewers can believe the noble man seen in the 1967 episode was the shambling, asshole-ish mess of far different motivations from the NG movie.
Berman, et al., would have been better off just using a little bit of imagination and creating some other sort of pivotal moment which brought the Vulcans to earth, rather than trading in on a well-known (to the ST part of the audience) historic figure. In other words, do your own thing.