Well as a new guild member I must point out that some costs for buildings on the beggining are a real theft!!! 5000 guilds ruines for a throne? We barelly were able to gather 600...
As you level and gear up, guild runes will come more quickly, especially if you're under level, but overpowered for an instance. However, even as a 70/70, I sometimes still get multi-drops from an instance boss 20-25 levels under me (EXTREMELY RARE though).
Also, level 57+ world bosses drop great big stacks of guild runes, 190 at a time (not a typo). Also, you get guild runes from Siege contribution packages, special runes that give 100 runes from some seasonal events.
HOWEVER, as a member of a guild that is fairly active in siege, I'll tell you that the REALLY, REALLY hard thing to get for contributions is rubies (mainly needed for guilds that are siege oriented).