Khan was trying to seduce her, nitpicking her painting probably wouldn't have helped. Plus, that he didn't immediately put on a turban once revived is another big hit against him being Sikh.
He may have been Indian, or engineered in India or perhaps just ruled there, but he still can't be Sikh or recognized as one because he breaks too many fundamental rules. IMO the best way to deal with it is to simply say Marla was he worst historian in the Federation.
Plus, I can't imagine Khan (either version) believing in any higher power above himself.