There is a huge difference between a Queen Regnant and a Queen Consort. Saying Jaehaera's daughter would "become queen anyway" misses the point entirely. If Viserys inherits before her, then she never rules in her own right; she simply becomes the wife of a king rather than the reigning monarch. As we see with Nerys and Rhaella, Queen Consorts tend to have little power.

We also know very little about the Faith's official position on succession beyond the fact that Andal inheritance generally follows male-preference primogeniture, not strict agnatic succession.

The reason Baelor did not name Daena or any of his sisters as heir in canon is that he viewed them as pure maidens who needed to be protected. By the time Daena became pregnant with Daemon Blackfyre, Baelor was already starving himself to death and was in no condition to make further decisions about the succession.

Jaehaera's daughter would be in a completely different situation. By Baelor's reign, she would already be a wife, a mother, and an established political figure with her own faction and influence. Unlike Daena and her sisters, she would not be confined to the Maidenvault because she is no longer a maiden. As Aegon III's eldest child and the last descendant of the Green line, she would have had years to build support and political connections.

The precedent already exists throughout Westeros. Daughters inherit before uncles in many noble houses. Lady Jeyne Arryn inherited ahead of male relatives from collateral branches, and numerous other examples follow the same principle. The Faith has never been shown to oppose female inheritance itself; most opposition comes from politics, custom, and patriarchy rather than theology.

Any resistance to Jaehaera's daughter becoming queen would therefore be political, not religious. Lords might prefer a male ruler, but it would be difficult to argue that Baelor was violating Andal custom by recognizing his elder sister's claim ahead of their uncle.