What happened to Thrall? We have no idea. It's very likely tied to the Wrath of the Lich King prologue, perhaps part of a soon-to-come new stage of the Scourge Invasion? We don't really know yet, but we're definitely going to be watching this. Thrall is kind of a big deal!
[Updated behind the cut]
Edit: Saurfang is missing too, but we know he's gone to Northrend, though that doesn't mean he's not going to be involved in something prior to Wrath as well. It also seems Apothecary Karlov was actually added in patch 3.0.2, and I was shamefully unaware. Apologies!
Edit #2: Thrall has begun respawning on all servers. Very unusual! These deaths were definitely not the result of PvP kills, he was simply missing when realms came up after the patch. Like the Scourge Invasion, he has spontaneously returned.