If anything, her negative experiences with the Bajoran Church could've been what compelled her to become more involved --trying to improve the institution from within rather than simply rejecting it full-stop.Kira's journey in that arc was realizing that the church's orthodoxy may not always be true and may represent institutional biases. But that's not the same thing as rejecting faith in the Prophets.
Remember -- she was excommunicated because of an accurate prophecy conveyed to an ancient Bajoran apparently by the Prophets. If anything, her excommunication would re-affirm her faith in the Prophets, even if it undermined her faith in the church.
Which, come to think of it, is probably exactly what compelled her to put on a Militia uniform all those years ago (as opposed to becoming a renegade survivalist hermit as many former Resistance fighters did).