Well...  Marrying into the clan doesn't necessarily mean marrying your cousin either though.  With as it was pointed out earlier, the possibilities of 100+ members of the clan, there are plenty of choices.  Besides, by your earlier logic, only every other to every third generation needs to breed within the clan to help keep it 'pure'.  The 'off generations' would be how the clan grows, otherwise it would trickle down to single digits far to quickly...  Or else a lot of cross-eyed twelve toed doujutsu users.  Lol.