While I too distrust many kinds of organized mega-religion, I don't interfere in other peoples' religious beliefs and activities any more than I allow them to interfere with mine. If she finds comfort there, then it doesn't matter what your particular leanings are....her religious life is about her, not you.
But, as Peter points out, if she uses these beliefs to shame you, or even if you're just sick of her trying to "convert" you, you will need to establish some boundaries, along the line of, "If you bring this up again, I am going to hang up/leave. I find it very uncomfortable and have made it pretty clear that I don't want to discuss this with you."
I know a few people who do the St. Joe thing. I've also, in my grumpy later years, learned how to say, "And, mom, was it St. Joe who spent ten hours painting the hall? The fact that you are completely discounting all the effort we've put in makes me not want to put in the effort any more."
You can say nothing and hold all these worries and grudges, or you can speak your mind and perhaps keep from slipping into permanent emotional separation from your mother. That's my two cents, at least.
Why not focus on your own happiness instead of on her glaring flaws?