When I tried moving Jedi Academy to the "steam" folder, it said I couldn't because the file was open in another program.
Shut down MBII Launcher, shut down all the programs that may have some of JA or MBII file locked, and try again.
I believe that moving Jedi Academy installation must be done using Steam software, not by moving Jedi Academy folder with Windows Explorer or any other file manager. Since I don't have Steam, I can't give you exact directions.
You also can switch to MBII Client instead of relocating JA directory.