I understand the fear of having your child indoctrinated, and I understand why everyone here is so sensitive to that aspect of the situation. Those of us born-in had a long road to deprogram ourselves, but the difference is we had to do it alone. Your child won't ever have to be alone in that task.
I don't think you should feel afraid to leave your child with his grandparents. As you said, aside from being annoying they are good people. It can be hard when you are leaving to remember that, because it's such an emotional process. Especially when you feel like you can't be honest about how you really feel.
The reason I don't think you should be afraid is because they aren't raising your son. You are. They may be grandparents, but ultimately you are the one raising your child, and will be responsible for whatever spiritual upbringing he has, and he will look to you for answers. If anything, it could be a good thing - compare and contrast what grandma and grandpa believe to what you believe, could give him a great education in logic and reasoning out how to form his own beliefs.
As someone who did a slow-fade herself, eventually you will come to the end of your road. I think it would be good to have an exit strategy. I feel like the situation of them "checking-in" on you is just the begining. To be fair, they are probably just thinking of it as doing their christian duty to check on your spiritual well-being...but it will keep happening. Remember they think they are saving you from eternal damnation. It's going to be emotional for them too.
I wish you all the best. This is not an easy situation for anyone to be in...but having been out now 10 years, I can only offer you that I am in a much better place now. I never thought I would be where I am now, or that the "fade" would eventually have an end. It was really rough, but the freedom I feel now to be myself - was worth every arguement, every hurt feeling, every tear shed between me and my family.
You and your husband will know when the time is right for you and your family to move on.