You can choose to protect your children, or not. Will it be hell for you to do so? Quite probable. That's your job, to protect your kids physically, mentally and spiritually.
It is quite possible to get the kids out now and remain married. The marriage will go through hell for quite awhile but if there is love there it can get better eventually.
You could try and keep it together and therefore you will have more control in their daily lives. Or should you separate every other weekend will be filled with jw activities anyway. Weigh all your options and have all your ducks in a row before you do anything. That would include checking into jw custody issues, an attorney who is familiar with jw issues, finances, etc...etc...
Give your kids a chance at a normal life and they will thank you someday for it. Keep them in the cult and one day you may be the one posting here bemoaning the fact that they are shunning YOU the apostate or spiritually weak one.
I wish you well no matter what you do even if it is nothing it will be difficult to live with.