Two guilds can go to war one against the other.
- Declaration must be accepted by both sides.
- Once the declaration is accepted, no recruitment is possible.
- War starts 24 hours after declaration, lasts 3 days.
- Gold and fame loss is halved, though the winner gets the full ammount. (it injects some extra gold in the economy, but I figure people need an incentive to fight in the first place)
- Total gold and fame from raids is turned into points. Guild with most points is the winner. Not sure about a prize for that, a badge or something symbolic should be enough.

Something similar has been suggested as a future update already, Pirate Code Wars, a link to the forum is below.
viewtopic.php?f=5&t=209&p=4441&hilit=pirate+code+wars#p4441

as far as the points go, are we talking tens of thousands of points or maybe only a few hundred?