Yes, if you are using a joint federal return to file a joint nonresident PA return PA will use all the income to figure a proportion of PA income (allocated in the PA interview) to total income. That proportion is multiplied by the resident PA tax on all income to arrive at the proportion of that tax that is PA.
The other option is to file a joint federal and a joint resident NC return and a separate PA nonresident return with only your income/deductions. According to PA Instructions here (see page 6), a person who does not live in PA or have any PA income sources is not required to file a PA return even if married to someone who does have to file a PA return.
In a desktop product (CD/Download) you would create/file the joint federal and joint NC returns and then create a "Mock" separate return with only your income/deductions. This would flow to a separate PA nonresident return. You will not be filing the "Mock" federal return so you will need to print/mail the PA separate return. Here is a link with more details.
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