Sorry for the double post, but I thought this information to be radically different enough, and important enough to risk such an act.
I quote Day of the Dragon, the first WarCraft novel:
"War.
It had once seemed to some of the Kirin Tor, the magical conclave of Dalaran, that the world of Azeroth had never known anything but constant bloodshed. There had been the trolls, before the Alliance of Lordaeron, and when at last humanity had dealt with that foul menace, the first wave of Orcs had descended upon the lands..."
If the Troll Wars happened 8,000 years before WCI, the wording of that passage seems a bit too recent... It sounds as if the Orcs had come just after the trolls, not thousands of years later. This DEFINITELY hints that there was another war involving trolls. Thus, the Great Troll War. Definitely makes sense now. Though only a scant few details may have been on that part of the Blizz website (accessible only via google... odd...) seem to have been correct details.
I'm not sure if Knaak is referencing the Alliance of Lordaeron as the one that is currently in place (at the time of the book) and that was formed during the Second War against the Orcs or if it refers to the force that defeated the Forest Trolls. Either one works, as what little information that link contained, it did hint that Lordaeron was again the focal point for an alliance.
Another key part of the quote: "... when at last humanity had dealt with that foul menace..."
That part right there makes it look as if the trolls were a great threat to humanity, and that the trolls threatened primarily the humans, more so than they did the Elves or Dwarves. Remember that in Blizzard's stuff on the Troll Wars, the trolls were more of a future threat to humanity when the humans united to crush them; they were not an immediate threat, and were definitely a much greater threat to the Elves. It's not much, but the style and wording of that quote definitely contribute to the fact that this seems to be a different troll war he speaks of.
In conclusion, I'd say that the evidence points to the fact that the Great Troll War is indeed real, and is viable in WC lore.