In GvG you score faction points (Balthazar faction) for killing players and NPCs (archers, henchmen, bodyguards and the Guild Lord).
If you win, you also get faction for winning.
It would appear that the amount of faction you win depends on how long you have been in your guild.
When I switched from one guild to another, I noticed that it had dropped.
Over the following weeks, it rose to 385 faction (or thereabouts) for a GvG win. However, I just swapped back, and last night when we won a GvG battle, I got 35 faction.

Hmm, no more swapping guilds now...
I will try to watch the increase and decide whether it increases per win in a guild, or whether it just depends on time spent in a guild.