I totally get the conundrum, but I would definitely say no to this one. Maybe just because I’m a Jewish atheist, but it sounds equally as important to you.
Our family has run into some other issues where my husband tried to get me to let stuff slide with his parents, to keep the peace, and I had to sit him down and explain that he needed to be my partner here, and his/my values should rule, not those of his parents. Since he agreed with me, he needed to stand united with me and not expect me to stay silent, or for me to have to explain our decisions alone.
We let small stuff go, like our kid watching way more screentime at my MIL’s house than we’d ever allow at ours, but with the big stuff, I think there’s a point where you need to be firm, and it shouldn’t all fall on you to do it.
But whatever you choose here, of course your son will still ultimately get to choose for himself. Good luck!