Given that it's currently not worth it to mine LTC using GPU, having a GPU miner out is not going to change much. But there are few potential problems I can think of:
1) This puts a cap on LTC price. When LTC price rises to make GPU mining profitable, we will see a bunch of people switching their GPU farms to Litecoin and sell the mined litecoins for bitcoins. This will put a downward pressure on Litecoin price. This is not necessarily a bad thing, because price doesn't matter that much.
2) Could lead to wild swings in difficulty as GPU miners move in and out of Litecoin mining. This will be similar to what happened with Namecoin before the merged mining. But since Litecoin retargets at 1/4 the time as compared to Bitcoin (3.5 days as oppose to 2 weeks), the swings shouldn't be that painful.
3) GPU mining makes it easier to 51% the chain. It would be easy for a decently sized GPU farm to 51% the chain.
I think I'm most worried about the last one.
Number 2 is the biggest danger. With the next Litecoin retarget, as long as price stays above 0.0015, it will be more profitable to mine LTC (yes, with that closed source miner). Maybe not this time around, but by the next time when more people will have heard of it, you could get a few hundred MH/s switching to LTC mining, reach retarget with a 4x difficulty in a few hours, and then they leave, which will then make it very difficult (2 weeks or more) for the rest of the miners to fix by retargeting to a lower (0.25x) difficulty. Also take into account that, at this point, it will be largely unprofitable to mine LTC even with GPUs, so you might have even more miners shutting down.
The difficulty swings that happen because of exchange rates have been proven to be non-converging. Profitable difficulty periods get shorter and unprofitable periods get longer. It happened to NMC, I0C, IXC, FBX and TBX in the same way. Eventually the chain dies, unless merged mining takes over. In LTC's case this is not possible.
We shall see. It will be at least interesting to watch.