I've used SMF for years and am currently an administrator on another website that uses the same version of SMF as here. I can say that changing permissions is not as difficult as it may seem. As a group moderator, yes you have to assign people individually and doing that for 100+ people can be a PITA.
However, we don't need to do it that way IF an admin can do it (Skuzzy). Side assignments are done by squad, so access to the Allied/Axis forum can just be given to the specific squad groups. For example, JG11 is assigned to the Axis for coming FSO. You just go in to the settings for the JG11 usergroup that already exists and add visibility to the Axis forum. If they get swapped to Allies, then you just tick the box for Allies and remove Axis. Doing that for 20 or so squads is much more simple than doing it for each individual person. The only problem is that it requires an admin to do it... which may be asking too much.