You asked for opinions, so here goes! The first thing I think you should do is consult a very good divorce and child custody attorney who is either willing to learn about or able to handle jw issues just to have her/him at the ready in case the worst happens. Second, start exposing your kids to crirical thinking skills and the real world NOW! Third, reiterate to your wife how her social standing will be ruined if/when you're df'd and ask her to compare you being shunned with how her father was treated by her grandfather. Then review the questions that you have with her. Fourth, send them to the elders and not the Watch Tower, so you'll be following the chain of command.
Then let the chips fall where they may. If she divorces you for doing exactly what she wanted you to do, then fight her tooth and nail for at least joint custody with you having decision making ability for educational and medical issues for your kids. Try to stay as calm and reasonable as possible throughout this process, so the kids don't become afraid of you. If it comes to all that, there are attorneys and counselors who can be provided for the children, and orders can be written into the divorce/custody agreements that forbid your wife to trash you for your df'd state.