GURPS isn't actually responsible for the Deceiver debate. It was alive and well long before GURPS ever came out, and was simply based around the conflict between the onscreen death on one hand, and the absence of any textual or pictorial reference to that death on the other hand. (Not even a shot of the dead D in the postgame pic.) Plus the reference to Myrdred's still possessing Soulblighter's crow, from a later journal entry.
It's pretty much the same as the Mazzarin problem. On the one hand, we see a Shade named Mazzarin working for the guy we know killed the famous Mazzarin; on the other hand, no one in-game seems to care about it and it never gets mentioned and it seems unlikely that Mazzarin would have let himself be Shadified. So which way do you lean?
Anyway, all GURPS did was continue the problem of refusing to mention The Deceiver's death while also refusing to explain what *did* happen to him. It was a slight boost for the "Deceiver Lives" side, but it's not like the conflict wouldn't have existed otherwise.
--SiliconDream