I'm new to modding on SWBF2 and would like to know if it is possible to make a Jedi with the clone trooper geometry, for obvious fantasy reasons :P
Yes. The way to think of it is that you can give a clone trooper a light saber, plus whatever else :)
You will want to look into modding the ODF files and learn the basics of "munging".
You can reskin jedi face for clone and give him gun here you can do what you have in mind many options