There's also a script here which you can use to auto-rename objects in MoI to have separate names:
http://moi3d.com/forum/index.php?webtag=MOI&msg=3114.5

To run that script set up a new keyboard shortcut and paste the script in, then you can trigger it with the shortcut key.

Also if you select all the objects with the same name and assign them a blank name that will remove the name, and objects with no name assigned to them will get labeled with separate cooked up names like "object1", "object2", etc... when you export to OBJ.

- Michael