It seems as if there should be an easier way to do it.
Maybe so. But every financial transaction of this kind has to be backed by official documentation -- and "net pay" is not an official measure of income under any rules/regulations. Otherwise, the reservist who fills out a W-4 form with 4 exemptions (and therefore has less money in taxes taken out of his paycheck) will have to pay back less than the guy who filed his W-4 form with only 2 exemptions -- even if they both earned the same gross income.