I wouldn't reply to the email. Anything you write in an email can be taken to the elders and is all the proof they need to df you.
Your wife's email shows she is not in listening mode with you right now. So stop talking. Nothing good can come of it. Focus on doing the best thing for your children. Her email, also basically says she is ready and willing to engage in a war with you for the children. This is not good for them.
Tell your children what you believe, calmly and gently, whenever they ask you or whenever the occasion arises. You don't have to badmouth your wife, or the JW's to your kids. You can just say to them, "that's what mommy believes, but I don't believe that." Tell them most of the people in the world don't believe in Jehovah. Plant little seeds of doubts in their minds that cause them to think and question everything. Explain to them how everyone in the world believes different things and that's OK. Keep at their intellectual and emotional level. Do not drag them into the war between your wife and you.
Children are pretty smart and if given enough information, and both sides of the story, they will be able to see what's what. They will be attracted to the parent who stays calm, reasonable, and doesn't scare them or make them feel sad. They will be attracted to the parent who makes them feel good. It may take a while to undo the previous damage, but be patient, it can be done. Many men lose this war because they give up entirely and give their kids over to their wives and their organization.