If it was a newbie mistake, and you know it was one, then that's perfectly understandable. The best course of action at that point would be to (POLITELY) teach them the rules of proper etiquette if they are willing to learn.
GG depends on the context.
You threw out WoW as an example. In WoW BGs (and everywhere else in the game) you are unable to speak to the other faction. In this case, when your communication is restricted to just one side, GG can really mean "good game" instead of "I surrender" or "I accept your surrender." Even so, it can be seen as a jerk move (depending on context) to throw out a GG if you're losing. If your intention is to say "Good game, well played guys. We'll get them next time," then it's perfectly alright. However, if you throw out something like "gg no re" (I surrender, I don't want a rematch), then that is totally a jerk move because not only are you saying it was a bad game, but you're also insulting the people who fought along side you.
Now let's contrast two other games as an example: League of Legends and StarCraft 2.
StarCraft 2 is very cut and dry; if you exit a game, then your opponent automatically wins and you are taken to the score screen. No further communication is possible unless you decide to private message the other person. Therefor, it is important that the surrendering player makes his intention known before leaving the game and the victor to wait for that surrender.
League of Legends is worlds different. If the enemy team loses their nexus or votes to surrender early, then you've got a few seconds left before you're booted to a chatroom with the entire game's players. Because someone doesn't automatically lose when they leave (they can reconnect at any time), the fact that there's a few second delay between the surrender/nexus destroyed and the boot to the score screen, and the fact that you have an after-game chatroom, throwing up a gg regardless of who won or lost is not bad manners. However it has to come after the surrender/nexus, otherwise it WILL be seen as a jerk move. In LoL's case, gg'ing before the enemy but after the surrender/nexus is perfectly fine as etiquette.
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