The general answer for a non-reciprocal state would be that you file joint federal and separately state. You would file a WV only return, and your wife would file a part-year resident WV and a part-year resident PA return. (Not non-resident returns, in her case). This would require 3 separate turbotax files so you will want to use turbotax installed on your own computer since online returns would have 3 separate fees. You would need a joint federal return with no state, a separate federal return for you with WV (print and mail WV and discard the federal return); and a separate federal return with PA for your spouse (print and mail PA and discard the federal).
Normally, if your wife was switched to WV withholding, you would only need to file a WV return due to reciprocity -- except that in this case, she would still have a half year PA withholding and the only way to get that back is to file a PA return.
I think, that at this point your wife should leave her taxation at PA and have it switched on January 1, since if she only has PA withholding, then she only needs to file a PA return and not a WV return when married filing separately.
Under reciprocity you could file jointly in WV only, and you can do that next year for sure, but that doesn't account for her PA withholding this year.
Maybe someone else will have an idea.
@Critter#2 ??
