You can still file with your spouse even if she did not have any income, assuming you met the substantial presence test to file as a U.S. resident.
If she had $0 worldwide income, filing together will be a benefit. You can use a larger standard deduction and the tax rate will be lower.
Should you get audited you will just have to show she did not earn anything. It’s hard to prove that, but you can show bank records and other financial statements showing no income received.
See Nonresident Spouse.
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