I agree that the Quarry seems like a massive waste for what it picks up. I'm intrigued by the idea of setting a filler up to replace all the trash it digs up, but there's also the potential of turning its output into scrap for a mass fab. Isn't that the engame of IC now?
Well, that's certainly one of the things you can do with all that material. Since I started using Forestry, I find I actually have a use for all the dirt and sand I might find, though.
Honestly, I prefer to fill any open pits I've dug - I hate turning the landscape into a giant strip mine, and usually I'm down in the Quarry while it works, mining whatever's visible on the sides and exploring any caves. So when it's done, there's literally nothing to see there, might as well get rid of it.