First off, you need to go back to the judge who signed off on the 50/50 split for custody. You need to stand up for your rights and those of your children. Have documentation of times your ex failed to deliver the children to you as agreed, his excuses for doing so, and how much you ended up having to pay him for child support as a result of these orchestrated violations of your custody arrangement.
1. He is in violation of the 50/50 custody arrangement, thus forcing you to make support payments to him. If you don't stand up for yourself, your ex certainly won't - in fact he's probably gloating at the KH about how you have to pay him because he's figured out how to scam you into getting more time with the kids than you, plus he gets to subject your children to JW indoctrination whenever he gets the chance.
2. He is in violation of the agreement whereby neither parent will pressure the children into religious practices. His doing so perpetuates his violation #1, and in turn violates your right to shared/equal custody and forces you to make support payments to him.
3. If you don't attend a church, then you need to provide alternate activities on KH days, your ex is going to take advantage of that by claiming that he is providing a social / spiritual environment that will be of benefit to the children. Would you not prefer to fork over money to Girl Scouts, Boy Scouts, sports activities, or other after school activitites that your children can participate in, instead of just acting like a victim and letting him take advantage of you, claiming that the JW Meetings™ and Field Service™ provide for the socialization needs that your children have?
A 50/50 arrangement should be just that. You get the kids for one week or two weeks in a row, he gets them for the same amount of time. Period. None of this him getting them for meeting nights, and weekends so they can go in service, so he can attempt to screw you over. No late or early pick ups or drop offs, because that will play into his attempts at screwing you over as well. You have as much right to give the children a break from the KH and JW activities (call it your "belief system" if you like) as he has to drag them to the KH and so on.
As to how to deal with your children - first and foremost don't give in to their father's bullying you so much. You can bet your bottom dollar he is taking advantage of that too and twisting every instance into an opportunity to berate you to them. He has them 51% of the time?? The kids will hear about how he does SO MUCH MORE for them than you do, and how you neglect them, how you'd just rather give him money/support payments to get them out of your hair. How you don't love them as much as he does. How he's providing for them spiritually, and looking after their Eternal Future™, whereas you are selfishly focused on the here-and-now. Fight for your kids. Being nice to a bullying ex just allows him to steamroller you into looking bad to the kids.
When discussing religion or belief systems with your children, teach them the importance of asking WHY. Teach them how to evaluate evidence. Teach them how to weed through baseless claims and require facts. It's more important for children to learn how to think - which is the course I'm recommending for you - rather than what to think, which your ex-husband is doing to them.
What I'm really saying - I realize I may come across as a bit harsh toward you and that is not what I intend - is that you are no longer a JW and you do not have to behave in a JW-like Submissive™ manner to your ex-husband. You may not even realize that his behaviour is bullying toward you because that is the dynamic you have become accustomed to from him. But it IS bullying. You don't have to put up with it. Not for one minute. Be the strong woman that doesn't put up with his crap anymore. Do it for your kids, and do it for your own self-respect.