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Your wife cannot file without your knowledge if you are separated.
I suggest that you go ahead and file as you normally would and mail your return in. Attach a statement to the top that states your position and you can attach a copy of any separation agreement that you have. File as MFS and, if the IRS supports your right to your own exemption, they will disallow her return and she will have to repay money that was returned in error.
Let me know if you still have questions.