Here’s where the controversy lies: Viewers have reacted on two fronts - one, due to how Islam and Muslims are portrayed, and then about the mere presence of those subjects in the first place.
So this sort of thing does happen. I know next to nothing about Mongolian culture or how they balance the reverence many apparently have for Genghis Khan with the historical reality that he had a lot of people slaughtered or enslaved, so I can't say how these same people would react to Jaadugar's depiction of the Mongols, but I imagine it might be the reason why it didn't depict Genghis Khan's face.