I'm going to ask for an expert here, @pk
As said, you can file married filing jointly or married filing separately. If jointly, you must report all your spouse's worldwide income, including income she earned overseas (you may be able to claim a credit if she also paid income tax overseas on the same money).
If filing separately, you report only your own income, deductions and credits.
However, if you file as married filing separately, your spouse also must file a US tax return. Since she passes the substantial presence test, she would be required to file as a US resident (married filing separately) and report and pay income tax on all her world-wide income. So there is not much advantage to filing separately.
https://www.irs.gov/individuals/international-taxpayers/substantial-presence-test
She might be considered a dual-status alien, which would allow her to pay US tax on her US income but not her overseas income, but this is complicated and I don't know all the rules. You say she is intending to return to the US as soon as approved? This might rule out the dual status situation. I need to ask an expert. @pk
https://www.irs.gov/individuals/international-taxpayers/taxation-of-dual-status-individuals
