Maybe say something like this: If your god truly is a loving God then he will find a place for me in your heaven, because without me there what kind of heaven would that be. I would certainly hate to go to a place where people I love weren't there too and if I'm made to forget them that would be a really dirty trick don't you think?

I think asking questions is the only option. Not too much against religion (you don't have to avoid it though) just firing her interest and her thinking. Try to find out what her picture of god is, where heaven is, but also why does god not help people, etc., etc.

Hypocracy. I'd sit down for a while and make a list of all those you can think of until you have a few to work with. Judgement comes right to mind. How does it work when they tell you not to judge others, that will be gods work in the end. Then as they preach they go through all the life choices one can make that they'll tell you will send you to hell. There's a long list to fill up a well there alone. Magic. How do you preach against the practice of magic while the son of god performs so many miraculas acts of a magical sense? He is a loving forgiving god, thou shalt not kill. While the bible is loaded with death and distruction by his own command. And will end time on this earth with death and distruction before sending us to hell. That's a loving forgiving god!?! Explain how christianity has killed so many in the past. ECT

Don't push, or tug. That's what the religious guys do, and by doing so, you are falling into their playbook. Just give her things to think about, things that interlock with good logic and let them percolate.

One question to ask and let her ponder (no answer necessary) is what is wrong such that she needs to pray for you? Are you unhappy, and thus in need of her help? I mean, she is trying to help you, but she's using a method you don't appreciate. If you let her realize that just being atheist doesn't mean you are unhappy, and that her prayers are apprecaited, but unnecessary (tell me you don't appreciate her being concerned for you?) then maybe, just maybe she'll realize that the prayers don't do anything for anyone but her... in fact, that is another question, does praying, thinking, about the situation help HER to feel better? If so... where is the harm in thinking about it (how to help mom)? That might actually be your hook: prayer is just a way to be calm and think through a problem until a solution comes to you. It doesn't have to be in any gods name.

Last thought: I get it, you don't believe. Will she really be harmed if she chooses to believe (assuming, of course, she chooses to be a good strong critical thinker who thinks for herself but just chooses to get solace through religion)?

?? Who is taking your children to church?
Just laugh and say Christianity is all nonsense, but that her positive thoughts for you (prayers) show a good heart.