But Keiko was the one who decided to talk about the bajoran religion in science class, that she calls the celestial temple and the prophets wormhole and wormhole aliens respectively doesn't change the fact that she was talking about the literal gods of the bajorans.
And of course the bajoran religion wasn't just a belief, they had actual proof their gods exist and the religion started in the first place because the prophets send orbs and visions to them.
When there's tangible proof and it is literally possible to visit the temple and the prophets and talk to them while using the runabout's scanners to collect data about them religion and science cannot be separated anymore.
Keiko was stubborn and disrespectful, there was a line where she pointedly said something like "the wormhole aliens who the bajorans believe to be their prophets ..." and that was really unnecessary and she only did it to piss off Winn. Keiko was wrong, she should have made concessions because when she decided to teach a mostly bajoran class about the bajoran religion she should have treated their beliefs with respect.