While this is an old, unfinished in game editor and I could only find the RC1 source code for it, the editor could be a very useful starting point for someone with some time to update, change, correct and finish the project.
The editor is in this mod and it appears to let you and others edit the map while playing. You can save and load a .map file which you then can copy in the .map file of the original map. Recompile and there is the.bsp of the map with a new item layout created 'in-game'.
This really want to set up q3map2 again....
Edited 56.63 minutes after the original posting.
I also worked out how to load changes with RC4. Basically, you need to save the changes as the same name as the BSP. That is, changes to
q3dm1 need to be saved as
\editsave q3dm1. The mod review has been updated.
There's a ton of maps out there that would benefit greatly from this mod. Many maps have really awesome layouts and designs that promote good gameflow but are sadly tarnished by poor item placement, and could easily be "salvaged" by doing nothing more than moving, adding, deleting, or changing items.