Since you both have MD income, file joint. Not sure about the MD state return, but I'm confident when you file joint, you can indicate you are a NR while your spouse is a resident. But regardless, no matter how you file the MD state return, your spouse files as a resident since that is in fact, their SLR and the rental income is in fact, MD generated income. Shouldn't be a problem for you to exclude your military income from MD taxation.
