I agree. This is not too dissimilar from if you were living in MA and traveled to TX for 6 months for a temporary assignment. Money earned in TX is still MA taxable income if you are living (domiciled) in MA when it is paid.
You might explain the situation and ask for a waiver (abatement) of the penalty. But I think you owe the tax.
https://www.mass.gov/info-details/amend-your-tax-return-or-request-an-abatement-of-tax#when-to-file-...
