When you cap the weekly restricted tomes for the week you get a bit of red text and the message "you cannot receive any more tomes of 'x' this week". Rather than that, however, why not use the tome conversion system in place when old tomestones are removed from the game?

Ex: 90 tomestones of Scripture -> 30 tomestones of Lore

"Weekly limit for allagan tomestones of scripture reached. Excess tomestones will be converted into allagan tomestones of lore."

This would just be a small addition to encourage participation in dungeons or other content after weekly cap has been reached.