Politeness only works if both parties engage in it. If your MIL is asking politely, she should be making it easy for you to decline, accepting a simple "no thank you" graciously, and taking a hint if your decline repeatedly. That's all basic. If she isn't doing all that, then it's not a simply a matter of you being polite or not.

But this seems less about politeness or even the specific issue of going to church and more about telling her that you're not religious. You either have to tell her not. If you don't, don't be surprised if she assumes you are and treats you accordingly, which includes cajoling you to "get right with God". Religion is a cult, and cults work by their members pressuring each other to get with the program.

But if you do tell her, don't be surprised if things go sour. Again, religion is a cult, yada yada. But that's go nothing to with you being polite or not, or how you tell her, or whatever. It's the substance of thing. Religion literally conditions people that it's fundamentally wrong not to believe. Depending on how strongly she feels that, it may be literally impossible to tell her you're an atheist this becoming a major shitstorm.