It turned out the assumption was wrong and yeah, you should remove the logic handling that once it's evident futures may go negative, and you should have a process capable of making that change with only a day or two notice. But being robust the rest of the time at the expense of mishandling a once-in-fifty-years event is not in itself a bug.
If you disagree, should a trading system also allow negative prices for precious metals futures? Stocks? Currencies? Options? Bonds? Futures on stocks or bonds? I can contemplate all of those trading negative in extraordinary, contrived scenarios but I would design systems today not to trade them at negative prices.