Ok ... you will not be screwed if you do things correctly ... if he works from home and never steps foot in MD then he should only pay NC taxes.
If the employer withheld MD taxes by accident then you file a non resident MD return and allocate none of the income there to get all your money back. Then fix this error with the employer so you don't have to file 2 states again.
If they do not withhold MD taxes on the W-2 then your mistake was way back in the MY INFO tab when you indicated you had MD sourced income so the program brought the MD return for completion ... either just delete the MD return and/or change that in the MY INFO section.