I'm not gonna talk about the compatibility of a fairly hypocritical catholic and a firm atheist, that's for you two to handle.

But regarding the sex I can just highly recommend clear communication. Sex isn't something you owe or are owed, but it is an important part of a relationship. You both have the right to not want sex for any reason, but you both have the right to be unhappy about it too. If you feel like not having sex for that long will make you unhappy, talk to him about it. Explain why it's important to you. It's important that both of you know what the other thinks about this. If you find out the abstinence is important to him in a similar way the sex is important to you, you two can try to look for a compromise that would work for both of you. And don't worry about changing your mind later. If you go with it but get too frustrated after some time, just talk about it again and how it doesn't work. If you care about each other, I'm confident you'll find a way to both be happy.

I honestly don't think his religion is that important part of this case. He could want to have a sex break for any reason and I don't think the result would be much different.

By the way I recommend also thinking about what you find important about sex, as sometimes intimate contact can be just as "fulfilling" as sex itself. But again, that's up to you to judge.