If you were married on December 31st, you can file jointly if you choose. Consider that you must use the same status as you indicated on Minnesota (MN). This status usually has the best tax advantage.
Your spouse could file married filing separately on the Wisconsin (WI) return since it's a choice on that state return. She would report only the income earned during the residency period.
You can create two accounts in TurboTax Online to review the results both ways. If you agree, decide which is best for you both and file accordingly.