Normaly he will be freed when you speak to him after freeing your friends from their cages. But there's a glitch, where they never get into the cage - it is triggered by saying "We mean no harm" when entering the secret academy.
So the big question is: Are your friends in the cages? Or are the cages empty and Kreia/Atton standing around at the entrance? If empty, try the fix on the [url="http://www.team-gizka.org/downloads.html"]Team Gizka Page[/url] - it's called Telos Academy imprisonment Cutszene Fix.
In this case, install the fix and either talk to atton (to get a "workaround" method) or load a savegame before entering the secret academy (to play the whole thing without problems). I recommend the last one.