Just make your map like this:
http://www.youtube.com/watch?v=4FTQ4I5FRys
If you want an isometric camera, make the map in a way that supports the camera. Don't make the walls higher than 64 units high, place the camera 128 units above the player. It is not hard. I mean if you don't want the camera to poke into stuff for a map designed for such a camera, make the map specifically for the camera.
If you are making a mod with an isometric camera in mind
and the map you made is causing the camera to poke into the walls then ...
On anohter note, the mod Error mentioned by Krimzon ...
http://qexpo2005.quakedev.com/booths.php?id=31
The night is young. How else can I annoy the world before sunsrise?

Inquisitive minds want to know ! And if they don't -- well like that ever has stopped me before ..