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@cmcgeehen wrote:

She is not understanding why she can't file with single status and completely exclude his income for the pro-ration.

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Single is completely wrong unless she was legally separated from the spouse under final judgement, which doesn't seem to be the case.

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Since she was married, her only option is to either file MFJ or MFS correct for MA?

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As explained in the original response.  If they don't have to file MFS unless the spouses do not share the same MA residency status/period.  In other words, if their residency status and period are the same, they are allowed to file MFJ.

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If she files MFS she owes more tax than if she files MFJ... especially if all of the income needs to be included in the NR pro-ration.

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What "NR pro-ration" are you referring to?  Please see my last response about the application of proration, which affects only the exemption and that the inclusion of the spouse's income should not have any material tax effect because she was both PY and NR, whose proration is based on day-count during the residency period (i.e. not MA vs income from all sources).