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.