In the very end, he is attacked by Illidan when he and other elves go too close of the new well of eternity. He wasn't killed, but imagine if he was. Illidan just killed the most liked guy in the world, and the leader of a country. He becomes so hated that even death isn't good enough for him and he is sentenced to being locked in a cave for all eternity, kept by the [[Dead Little Sister sister of Jarod, Maiev]]. When Tyrande freed Illidan in Warcraft III, Maiev is so angered that her brother's murderer is free again that she doesn't hesitate a second to follow him thousands of miles away, even if he was freed by the night elves actual leader. She also has no problem letting Tyrande die and lying to Malfurion just to kill Illidan. Finally, it explains why Jarod doesn't show up in Warcraft III or ''WoW : he's dead.
On the other hand, look at the actual situation: Jarod is not killed by Illidan. Illidan suffers The Punishment "just" because he created another well, and while he had a quite good reason to do it. Jarod just disappears and nobody seems to care or, as the official story says, "One day he simply vanished, along with a few personal possessions. He did not say where he was going, nor, in fact, did he bid anyone farewell. Since that time, there have been no sightings of him."
Maybe Knaak felt attached to his character, or maybe he didn't want to end the books on a low note. At least, that's the impression I got when I read the novels.