If your main concern is your children then leaving your wife will likely only make it much harder to prevent their indoctrination. She may take refuge in the organisation for her loneliness and grief at your leaving.
It sounds to me like she is not really serious anymore about the religion anyway if she's not out in FS. She's perhaps mostly only now going for the friendship and community it offers (like any church does.) Seems almost that she is trying to back off the religion as much as she can to accommodate your needs. Cut her some slack on that regard, and don't get so hung up on a 5 year olds comments about Christmas.
It sounds like your wife still loves you very much but the real issue is youre not meeting each other's needs sexually (common with having young children and arguing over them). Make it a focus to discuss this frankly and honestly together. What exactly is the problem killing the passion. Has she put a lot of weight on after the children and you resent it especially since you've lost a lot of weight running etc?
It sounds like you are very numb emotionally, although otherwise quite motivated and energetic. You feel nothing much for your wife, get irritable at your 5 yr old daughter, and theres the comment you tacked on the end of a paragraph out of context that your little son clings to your leg crying wanting you to pick him up (why would you let him cry and not just pick him up...1 year olds need to be picked up and held a lot?). This all says you're emotionally shut down.
Please...NEVER argue with each other and raise voices in front of your little children. Can't emphasise this enough.
It sounds like you may be on the wrong medication tbh. Some anti depressants work by shutting the emotions down. The active ingredient in many does just that, numbing you mentally and you're ability to respond emotionally and empathetically. Strongly recommend you talk to your doctor and counselor about all this...they may feel you need to switch to something else.
Otherwise, trust the instinct that is telling you not to leave your family and little children who love you dearly. Work on your sex life with your wife, and on whatever is making you feel so numb and irritable towards her. If you are holding her in bed then there is still strong love there deep down. Cling to that feeling and work on building it.