Actually as I read through this post I was thinking he might have been using Sectumsempra. At this point, lets assume he is 16, he might have been working on creating the spell. Granted it would be a messy way to get rid of the flies, but they were an easy target and he would have to have somthing to practice on. Since the book belonging to Snape that inadvertantly ended up in Harry's hands was a 6th year book, I think this is a possibility. The books never say when he created it, only that he did.
That's a really good idea now that I think of it. Even Snape *probably* wouldn't dare to test out his spell on humans yet. I think it's a good theory that while he was creating the spells he was testing them out on flies and the like.

Unless, of course, we are all just over analysing everything!