Maya constantly says there is no God or God is dead, but to reset the world she prays. It's weird.
Those sound more like the words of someone who feels betrayed by their god, possibly to do with the fact that the Sensei we know seems to be different than the one that came before the events of the game, than someone who truly doesn't believe in one. She could be a believer who thought her god would save the Sensei she knew, and evidence suggests she loved, and then realized that was not going to happen so easily. When he did come back, but as a totally different Sensei, she could have seen it as a betrayal by her god.
Perhaps it's a habit, perhaps it's because of her being a shrine maiden, or perhaps she knows more than she's willing to tell us
That last part is pretty obviously true, she definitely knows more than she's willing to say, at least to the current Sensei, possibly to avoid losing him again even though she is aware this is not the same man she once knew.
Perhaps a dead god can be revived through devotion.
Maybe, or maybe the one she prays to now is not the one she says is dead, but one that she believes could bring the old Sensei back. One that has the power to do greater things with greater devotion from the follower it is doing them for, like bringing someone back from the dead or from a personality change caused by an incident. She seems to have absolutely zero actual medical knowledge about how the mind works, so she possibly turned to a new deity to try and get the old Sensei back.
