I think people are overestimating the perceived "outrage" over Great Prophets having unique abilities, just as people overestimated the outrage over Great Prophets being named. We've known that Confucius and Saint Irenaeus are in the game for an entire day, yet no Confucianists or Catholics have formed any angry mobs outside of Firaxis' offices!
I would actually see it as a sign of great respect if Firaxis did the research for each of these religious figures and found theologically appropriate abilities for all of them. I'm sure I'm not the only one!
There is one, uh, "religion of peace", whose followers have been known to issue death threats and worse when the prophet for their very peaceful religion is depicted.