So your issue is that now you have a tax return that has more federal withholding than it does income so its not able to be Efiled.    Thats an IRS limitation. 

I have the same issue with returns that have large NOLs that wipe all the income out, but they have withholding from W2 income, we end up having to paper file.

I guess a workaround could be to input some hobby income that makes their income exceed the federal withholding amount, that wouldnt create any tax liability but would allow Efiling.