Not a good situation at all -- I feel for you, outsmartthesystem. But, seriously, you are the spiritual head of the household -- in JW parlance. You are within your right simply to forbid her to take the children to meetings and the Elders should back that up (I recall a similar situation in which a non-JW forbade his children to attend; the wife objected, but the Elders took his side).
Play tough. Tell her, "I am the spiritual head of this family. You are subject in this regard to me. I shall decide where the children learn about God, if at all, and you will obey you family head. Otherwise, I shall contact the Elders regarding your lack of submission." You might similarly forbid her from going in field service, then use that as a bargaining chip.
It's the Chicago rules: they bring a knife, you bring a gun. I speak metaphorically, but not less seriously. Good luck.