Filing a joint VA return and your wife filing a MD MFS return is the best.
Virginia has two types of resident, domiciliary and actual.You are a domiciliary resident since you live and work there. Your wife is an actual resident as she was in VA over 183 days. From VA full year resident instructions, see pages 5 & 6 for full instructions.
Because you both qualify as full time residents, you can file a joint VA return and then claim credit for the tax paid on the MD return.
The MD directions are clear for married couples living in different states, your wife should file separately. See page 4
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