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If I were you, I'd try it both ways as the Joint return tax brackets are a lot more favorable. Also, if she files Married Filing Separately she will also lose the benefit of several other deductions and limitations.
It would be a simple matter for her to complete her return without you & your figures using the Married Filing Separately Filing status, note the tax & then add you in switching to a Joint return & see which way produces the lowest tax.
Normally, that will be the Joint return filing. It may not seem logical to you, but that's the way it normally works out.
Just checking in to see if I can assist you further.
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Thanks very much, Steve G.