Yes you (or more specifically, your spouse) will have a Maine Non Resident return to file that should only include your spouses maine earnings.
And, NO, your earnings are safe from ME. Maine does not tax income not earned in the state on that non resident return.
For instance, (make an assumption for illustration) all your earnings are NH, your spouse has PT earnings in ME and part time earnings in NH.
federal return will includ ALL three sources.
NH has no income tax so none of these sources gets income taxed in NH.
ME gets thier tax ONLY on the ME Earnings of your spouse on a NON_RESIDENT return.