Why just junk it? Open up the CK, find a place to display it (your home, the library in the college of Winterhold, wherever), and set up a display case as an activator. Then place the scrolls you want to ditch inside, make them initially disabled - then write a basic script that, when activated, removes it from your inventory and enables the one in the display case. Then when activated again, if the scroll in the case is enabled, disables it and adds it to your inventory. That way you can take it in and out whenever.
Yeah, you could just remove it from your inventory, but it's an Elder Scroll. Treat it with some respect instead of just chucking down the hole in the nearest outhouse.