In a situation like this there are many different ways of handling it, and what you have done is just fine, even if a little frustrating.
To the extent that you wish you were able to have less of a refund from Maryland so that you do not have to expend additional money while you wait for your refund (in other words, if you withhold less then in theory more will be available to pay to Delaware), you can ask your employer to decrease Maryland tax withholding.
It is always a good idea to complete your non-resident tax return first. If, in the future, you and your wife do end up owing Maryland income tax for her work, you would want to make sure that on your Delaware return that you claim a credit for taxes that you paid to another state, in this case, Maryland.
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