These disjoint, disorganised movements exist to try and avoid another issue; that of a single person or group of people who can be 'discredited' or attacked by their enemies.
If you have a proper structure, you provide targets to discredit in order to bring down a movement or group. Groups like Occupy and Black Lives Matter and whatever else don't want a 'pope' like figure that the media can focus all their efforts on attacking, nor an organisational structure that can get infiltrated or corrupted.
Unfortunately, that causes the trade off you mention; you have no way to control the message your movement sends. This is what's caused so many problems with GamerGate as well, the fact it's entirely based on a hashtag and a loosely associated bunch of forums and blogs means that their enemies accuse them of absolutely everything they don't like that day.
But it's a trade off. Either have it decentralised and avoid the issue of a single leader/organisation being a media target (but lose the ability to control the message and who's involved) or have it centralised with a clear leader and structure at the cost of these people getting attacked non stop by their enemies and people trying their best to decredit/arrest/potentially kill them.