That's a bit naughty really. The same happened when Weymouth got themselves in trouble in the Conference a couple of years ago. They lost all of their first team in the middle of the season and had to play the youth team in the next match, which Rushden took advantage of and won 9-0 I believe. From then on, although they managed to get a few players in to help them see out the season, they were pretty much the whipping boys for the rest of the season, getting heavily beaten regularly. This put teams they had already played twice at a definite disadvantage, and could be argued changed the promotion places to some extent.
The league should not allow teams to continue to play matches in these circumstances. If they intend to resign from the league and accept relegation at the end of the season, they should be made to resign immediately, with their results being expunged so the potential advantage to be gained is averted.