Like i said, powerful aliens or gods are just nouns.
Can Starfleet do what the Prophets do? Sure. Starfleet can go back in time and change things. Starfleet can use mind probing devices to enter peoples minds and make them see visions. Starfleet can wipe out an entire fleet if they have enough ships themselves. Same can be said about the founders, except that founders can change shapes and doesn’t age.
But there are things fundamentally different about the prophets that makes them closer to the concept of gods. Prophets are omniscient, omnipotent, pretty much omnipresence, and in a sense omnibenevolence (as opposed to the Pah-wraith). Pretty much the qualification of “godness”.
Whether one chooses to consider them as gods is pointless. It doesn’t matter what its called.
As for Kai Wynn, I think her evil comes from her political desires, and manipulating religion to achieve her political goal. I actually don’t think Kai Wynn is ignorant. She is just very good at ignoring facts that is not beneficial to her political purpose. It’s not the religion that caused Kai to be evil. Just like there are starfleet admirals that does evil things, but that doesn’t mean starfleet or admirals are inherently evil.
The Chakotay vision quest stories, besides being weak stories, doesn’t portray future Native-Americans who lived in the DMZ in a particularly bad light. Vision quests are induced with a rather non-traditional “high-tech” device. At most it is a form of meditation. Other than the vision quests, Chakotay doesn’t seem all that concerned with religious to me.
But then of course humans in Startrek always makes fun of the Vulcan meditation. And in reality, Vulcan meditation and everything around it has a sense of religion to it, though they don’t believe in god or gods, but they believed in achieving logic. Which is the core of the Buddism belief. Yet no one would say that portrayed Vulcans in a bad light.