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).
That's why I find it hard to believe that his behavior was so harmful to the organization.