Basically, you'll file joint on the federal side of course. But on the state side your wife "may" also file joint as a non-resident of that state, and state taxes will be paid "ONLY" on the income earned in that state. It's important to note that since your wife has no choice in the move for this internship, that makes her a non-resident of whatever state she ends up in. Therefore a state non-resident return will be filed will that state.
Now for that state return you'll need to determine if she should file only that state return as MFS or MFJ for the best tax benefit. It will just depend on the state, as to which is best tax-wise.
