You don't joint file in IA, which only allows single filings although the paperwork sometimes seems to suggest it does accept joint filings...I struggled with something similar, with my wife having a taxable farm in IA but residing with me in no income tax FL.
In my case, Turbotax recommended that I do a separate single federal tax for her in which I put in only the IA relevant income. I then discarded the Federal form from and submitted the IA portion to the Iowa tax authorities.
Worked for me. I don't know if this approach would be relevant to your situation.
