I have a similar situation to yours. When my son was 3, I felt like you did, only it was my FIL pushing Islam on my son. My side of the family is non-practicing Catholic/Christian. Nobody goes to church, but there is a deep belief in God and "doing unto others..."etc. I, personally, do not believe in the "Western" notion of God and consider myself agnostic. My FIL is Muslim, practicing, actually a leader in his local Muslim community and my MIL is Catholic in her heart, but converted to Islam when she married my FIL over 40 years ago. My husband grew up going to Muslim school on Sundays, etc, but now as an adult is also non-practicing, possibly even agnostic like myself.
Religion is not practiced in our immediate household, we got married in a civil ceremony and there's no "prayer" of any kind in our home. But I always said we'd expose our kids to everything. So when my FIL started taking my son to the Mosque every time we visited, even though I was really uncomfortable (much like you are now), I let it go. My parents would occasionally ask me "don't I want to get my kid baptized?" "Absolutely not" is usually my answer. BUT we did send one of our daughters to Catholic school for 2 years (the academics were so good and our public school was so not good). And all 3 of my kids went to a Jewish pre-school. We also visit the Far East to see my parents, so they've been exposed to eastern religions as well - they've visited as many temples and shrines as they have churches and mosques. So I think we're doing a pretty good job of exposing our kids to the various religions out there.
Even though I don't believe in God, my kids do, and I would never change that. This is their choice to make. I understand your discomfort with your mom exposing your son to *HER* religion, but that's part of who she is. It's something they can bond over. You should have your husband take your son to a mosque to expose him to HIS religion. It's not just about religion, this is part of his cultural heritage, too. When my son was 3, I felt really weird about him going to the mosque and learning about Islam from his grandfather. Now that he's 13, I'm ok with it. And he and his grandfather are very close. We live in a very Jewish community and although we are not Jewish, many of my daughters' friends are. Add that to having spent 2 - 3 years a Jewish pre-school during their early childhood, they have probably more exposure to that religion than any other. Needless to say, my oldest daughter wants to be Jewish. My youngest wants to be Catholic/Christian because of the whole Christmas thing (which we do celebrate, it's part of my family's culture). And my son is very interested in Islam and Christianity and ways to bridge the differences so we can all get along. I think it's pretty awesome, actually, that by being exposed to the various religions, they have a total and pure acceptance that there are different religions/cultures/backgrounds and there's nothing to discriminate against or "be afraid" of.
There's no way to avoid religion, and banning it from your child will probably do more harm than letting him get exposed to it. The most influence comes from YOU, so whatever your mom *tries* to get him to believe won't really matter if YOU don't follow up with it. If I didn't want my kids exposed to any religion, trust me, it would all have been nipped in the bud and my kids would be staunch agnostics/atheists today. But I didn't want that for them. I know that many people get comfort from their faith and I want my kids to have the opportunity to choose that if they desire. I chose not to be religious - I made that choice at about 14 after a lifetime of being Catholic. But I won't choose for my kids. That's on them.