Akatsuki, beside collecting souls by killing forest creatures, maybe Akatsuki themselves should have special missions that reward you for soul. Exchanging souls for items might be nice thou the price for everything in Akatsuki will have to be increased.
For the good guys, we can have ANBU. ANBU members don't not abtain reward points from killing forest creature. If you want points, you will have to go on a mission. You will gain "scroll"(s) by completing a mission. You can exchange these scrolls for special "ANBU only" items.
All missions (both Akatsuki & ANBU) don't reward you with tons of exp, gold or gems, just credits (souls or scrolls).
If these does get added into the game. Special events that only trigger when the player is a member of the ANBU or Akatsuki will be added as well to enhance the exprience of the game. (No, not to add more exp to your character! =p)