First, I am not IN a fleet, and do not really have the time to participate in fleet activities.
My thought: If enough members of whatever super-hyper-mega fleet that is so Bad that they already own two harbors, and everyone else is to afraid to attach them really REALLY want to do HA, let them split off and join anothjer fleet, or create a NEW fleet... maybe they can even get enough members t o attack superhyper and take away one of those two harbors.
Of course, we cannot have members creating new fleets every couple days to allow mor HA, so maybe a limit, a player can only join a fleet once per month... you can quit anytime, but if you quit a fleet to allow your new fleet to do HA (or for whatever reason), you cannot return to the old fleet for a month.
That might also tend to moderate fleet size... those who want to do HA and cannot because their fleet already have two will create a new fleet, those who are not in the 35 players can get a new fleet, and those who want to be active enough to put in the effort can play what they want to.