I searched the forum if he has any dialogues or some quest and among the messages (but there were no any questions about his dissapearing, but still) the following:
When I take the quest and the crowd goes for the rune, I just teleport to the black troll's lair, run in for the rune - there's no one there yet, Agon is waiting at the exit, but I ignore him and after I take the rune I just teleport back to the monastery.
After completing all the quests to join the monastery, all the novices return. Agon is simply silent.
Alas, Agon simply disappears when moving to the second chapter.
That means he dissapears in the second chapter, I don`t know why. May be you`re right - he is killed automatically by the game...