So right now the way Raid completion is set up there is no difference between a guild that completes the raid in one refresh or one that takes 2 refreshes.
This is because you can start a raid the same the day you finish. (This is a good feature)
So the points you get for a raid it should be more if you can complete it with less refreshes. Say you lose 5 points for every refresh. This way you can better differentiate between the abilities of guilds.