I think I read somewhere that in the case of negative balance bug you need to rebuy missing coin (LTC in your case), or Cryptsy won't allow withdraws. It's quite a minor sum, why won't you buy that 0.0001 LTC or something?
Yeah. It seems they kept the coins as hostage and released it only when I paid that negative balance.
It seems they screw some people who leave a buy/sell order and never login for a long time and give them a negative balance

I'll never use that crappy exchange again...

I also got negative balance once, but long ago, in December. It was because the same order was executed twice for some reason, so it's not really a scammy behaviour, but an annoying bug (as the price can change wildly, but you should rebuy the coin).