Another case where the children will unfortunately get caught up in the middle unless you strategically and carefully guide things otherwise. Much sound advice has been given as to what you portray to your spouse as to your mental health. In a custody dispute she will certainly try to discredit your parenting abilities because of it. DO NOT BE ABUSIVE in actions or words towards your spouse. I know it is hard. Strive to be mild with assertiveness. Document every single detail and interchange between you. Use this very thread as a resource.
Your children are going to get caught up in the character assasination because it is inherent with every narcissistic parent operating under the sectarian dogma of the WT. "We are right, everyone else is wrong" Your children are already displaying and voicing the alienation tactics employed by their mother to tear you down and equate you with a perceived nemisis, namely Satan the Devil. DOCUMENT THESE OCCASIONS.
It may seem impossible to you but you will be in a better position to help your children if you are present in their lives at every available opportunity. I you and your spouse separate, with the children at such young ages, it is hard to say how much opportunity you will have to visit with them. Perhaps you can acheive some type of peace with your spouse by refusing to pit the children against you by alienation tactics based upon the religion? You agree not to attack the religion, she agrees not to attack you and your stance transferring her position unto the children.
I would strive with all diligence to find a middle ground now with your spouse while the children are at such a manipulative age. When they have matured into their pre teens and start to develope reasoning skills, then you may want to take the more drastic action of separating the entire family. Even then, it will create huge amounts of turmoil for them as they will no doubt want to please both of you.
Do not allow yourself to be vilified. Be strong and research others who have been down your road. Consult with a Family Law Attorney who has background in dealing with religion and parental alienation issues. Plot out a course of action that looks into the future and do not get entirely caught up in the frustrations of the present. Slow, methodical, educated, confident steps will help you to keep your children under your fatherly wings and draw them closer to you. Let mom take them to meetings without a battle, and in turn spend as much time with them in normal life activities as you can. I promise, they will remember those times as they mature and even if they are receiving negative press about you from mom or her friends they will always trust you and want you in their lives. You may not be the Spiritual JW Head of the household, but it is YOUR family and you can still be an incredible Husband and Father.
My thoughts are with you and your children.