There are plenty of mods that edit the appropriate .xml files to remove the compass from the HUD. At the moment, I'm running http://www.tesnexus.com/downloads/file.php?id=32092.
However, all that I've found remove the compass from both the normal HUD, and also from the bottom of the inventory menu. Is it possible to remove the compass ONLY from the general HUD and not the inventory menu?

Not sure if any released mod does this, but the upcoming version of HUD Status Bars lets you move the compass to wherever you want, or hide it, and this only affects the gameplay HUD, not the menus. I expect HUD Status Bars 5.0 to be released in a couple of days - possibly tomorrow.