Assuming he is a good guy, and there's no dark secret, he'd be especially upset that she was making a breakthrough on her own and he stopped it.
I wonder if it's more twisted than that. He wants him to be the object of her affections, not god. When she says she was about to pray, he says "no, no, no, no, no, don't you... that's my thing". His instinct is to turn her away from god and back to him.
But - it's a good thing for Fleabag that he inadvertently (and ironically given his job) saves her from finding religion. Fleabag is an atheist, turning to god would be a distraction from healing and understanding her place in the world.
He manipulates her into being vulnerable, and he could have gone down the path of conversion just as easily as sex. Neither were what she needed. She does need a friend however. Perhaps the show can redeem him enough that they can find a way to that, but only if she's stronger and stops feeling she wants or needs him. He needs to eat some serious humble pie!