You can either file married filing separate, or file joint and you can file as an injured spouse. If you file married filing joint and do not file the injured spouse form your combined refund WILL go towards your spouse's back taxes. Keep in mind that this will delay your return by approximately 14 weeks.
Here's more information regarding injured spouse relief:
https://ttlc.intuit.com/questions/1910698-how-do-i-file-form-8379-injured-spouse-allocation
