The decision to file jointly or file separate has many considerations that depend on your situation. This TurboTax link Should You and Your Spouse File Taxes Jointly or Separately? explains the advantages and disadvantages of filing separately vs filing jointly.
You may also want to consider filing as an Injured Spouse. An injured spouse is a taxpayer who files a joint return and all or part of the portion of the joint overpayment (refund) is, or expected to be, applied against legally enforceable past obligation of the other spouse.
This TurboTax link What is IRS Form 8379: Injured Spouse Allocation has information you may find useful
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