Try looking at the entlist in the .bsp file, locate the # of the ent you want to remove, and then use remove_entity.
If you don't know what the entlist is, just try opening a .bsp file in wordpad. You'll get a dumpload of jibborish, but if you scroll down about halfway through the crap, you'll run into a list of entities. Just remember, don't save it after you've opened it; just copy what you need.