The problem is that RMS undermines the FSF's progress by being a dumbass. No one's expects him to solve a moral issue, they expect to him to avoid harming their mission by being a ridiculous troll.
Their mission is his mission. FSF didn't hire Stallman, he created it. I think it's baseless to say that Stallman is either trolling or harming the FSF.
He created it more then 30 years ago. It has evolved into something much, much greater than himself and so the organization has a very serious responsibility to more stakeholders as well.
It wasn't harmful as in it would kill the organization but I believe that a lot of people were turned away from the FSF or even FOSS entirely due to RMS' behaviour.
Also lets not pretend its just RMS. ESR has been ostracized for his weird comments and behavior as well. The presentation of this as without precedent is really disingenuous.
Has it flourished? If we use the GPL as a barometer of FSFs success then it's going downhill. Apache and MIT licensing is on the rise dramatically while GPL is a decline proportion wise. On the other hand companies that want a GPL-like license are finding the GPL not strong enough (MongoDB).