First understand that the SLR for a non-military spouse does not change when they marry active duty military. It's not something that occurs automatically. So if your spouse's SLR was OK before they married you, then it's still OK now until physical action is taken to change it. I note you also don't mention what your HOR is. I can't assume it's TX just because you're stationed there.
In a nutshell, MSRRA doesn't help since TX does not tax personal income anyway. So OK can (and will) tax the non-military spouse on all of her income. That's the bottom line at this point.
You can check with base legal and you'll find I'm right. I realize tax season is over and the free tax help may no longer be available at the legal office. But you won't know if you don't at least call and ask.
Now for your federal return, you will and should file as MFJ no matter what. If you file separate, you will both automatically lose quite a number of deductions and credits you may otherwise qualify for.
