Hi Paul,
This is a tough situation and one that I am all too familiar with. I think that your note to your mom is good. I have just one comment about the following line:
I do not feel it is appropriate that you force your opinions upon him at this stage, particularly as he is too young to be able to identify the rhetorical fallacies in your arguments.
The second part of this comes off as a bit of a dig at your mom's beliefs, which she may take personally and use to play the victim and make you into the bad guy. Your mom knows exactly how you feel about her beliefs, but any percieved attack on them might trigger the persecution complex and encourage her to find ways to secretly preach to him.
If it were me, I might instead turn it around and highlight that her attempts at forcing her opinions upon him speak of a lack of respect for your rights and duties as a father to raise your child.
Just a suggestion. I hope that you're able to nip this before it becomes a real problem.