Are you sure you haven't scaled down some too? What kind of vis did you use in the compile before the last one, fast, normal or full. The more accurate vis the more leaves created.
A fine trick to reduce leafs is turning things into func_walls. I don't mean small details, but also complex archtitecture, try to make your room as square as possible if those entities are removed.
I've done it in my map
Ocean Temple, and by that I saved my map from the same error, it has 11000 leafs now, Hl1 couldn't take all the leafs it would create if some of the archtitectue was solid. Those arches above the golden fish heads, they are entirely out of func_walls and so are the pilasters that hold them. To vis that hallway is just a bland cubic room, if I hadn't tied those arches to an entity my map would never run.
Don't tie each brush to a func_wall, tie a group of them, just make sure they don't spread over too much space. The problem with entities is when a simgle part of them is rendered all of them is rendered, even if it's invisible to the player thus raising the R_speeds consideribly.