Has been a while since I watched it...yeah, I suppose she did believe in the Prophets.
But her machinations were about power, and greed, or any number of other "bad" motivations, all the while she pretended whatever bug was up her butt that day was due to some religious issue. Which has real-world parallels, to be sure, but we've seen plenty of that, and it made it "okay" for our heroes to oppose her. But what if everything she said was true at face value? That she didn't want Starfleet to do A, B, or C truly because of religious reason X, Y, and Z? Something that doesn't make sense from Starfleet's POV? What do they do THEN? They toyed with that a little at first, but it was all undercut when her true motivations were revealed.
I really liked Kai Opaca. It was a waste to kill her off immediately.
She very much believed in the Prophets. She also believed that she was the one to lead Bajor into a new era and show them the path to the Prophets.
She felt that Bajor was moving away from them... that the resistance felt that it was them and not the Prophets that caused the Cardassians to leave. She didn't like the idea of Starfleet or the Federation being looked at as a savior either. She didn't like the way Starfleet discribed them as "wormhole aliens" or their scientific approach at studying them.
She felt that she was one of the few that could lead her people back to the Prophets. That it was her duty; no matter what Machiavellian machinations she had to resort to.
That path itself is what made her arogant and greedy for power. The more she attained, the more she wanted.
She became very jelous that the Prophets had chosen an off worlder as their emissary. She began to resent Sisko because of it. Yet, she still listened to him for her people. Bajor instead, did not join the Federation, and signed a non-agression pact with the Dominion.
She still felt slighted, after all of this, the Prophets did not speak to her. Not when attempting to consult any orb. Yet they would talk to Opaka, they would talk to Bareil, they would even talk to Kira and they certainly spoke to Sisko regularly.
When she was finally spoken to, it was the Pah-Wraiths that did it. When she felt that she had betrayed the Prophets and Kira suggested that she step down as Kai, that was it. The Prophets had never offered her anything and she was unwilling to give up her power.
Only then did she turn to the Pah-Wraiths... in her resentment toward the Prophets. She hated Dukat, and only followed him because the Pah-Wraiths had told her to expect a guide.
In the end, she realized that she had been wrong and helped Sisko... thus helping the Prophets.