You can file a paper return filing married filing separately and include a letter to the IRS stating that you did not agree to submit a joint return.
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Only a family law attorney can advise if her actions will aid you in getting your children back. Deceit might mitigate in your favor.
As to the money issue (i.e. the refund) has there been any marital settlement agreement? In dividing property, you can ask for your share of the refund.
I doubt whether it would change the family court's ruling, unless she gets charged with tax fraud. But if the income info she reported was accurate, she won't get charged with tax fraud. Maybe she would have gotten the same refund whether or not you signed it or whether or not she claimed MFJ or MFS status. Did you file your own return? If not, maybe you should.