I don't really understand the inner workings of those transactions (and I'm just discovering about relay fees), but I guess if there was a way to make the transaction fee work per receiving address (like, sending 0.000001 LTC 100 times to different addresses or even from the same address to the same address = paying 100*0.1=10 LTC in transaction fees) this would impair his ability to cheaply make large transactions while not being an issue for legitimate users.
Here's my latest thought. I can force a transaction fee for each output greater than 2. Normal users will only send transactions to 1 address with a address for the change. Only advanced users will use the sendmany api to send coins to many address at once. I can force a fee to use the sendmany feature. So for every output greater than 2, you have to pay an additional 0.1 LTC fee. Without the ability to send to multiple addresses at once, I don't think the spammer can bloat the chain cheaply anymore.