To have a group of protestors who volunteer for a commonly accepted goal among them be organized, functioning and effective without hierarchical structures is vastly different from having a whole society functional and effective without hierarchical structures. What every system first and foremost must face is how conflicts are resolved, because conflicts of every level of severity will arise without fail. A group without conflicts, that exists exactly because it is made of people who truly think exactly alike, like HK protesters, is not a good example. ANY group of people who truly think exactly alike is perfectly functional, no matter what it is they collectively value.
It sounds like the problem then is getting everyone to share fundamental values. If everyone has common ground to start from then it's easier to build towards a resolution of conflict.
I agree that any group of people will eventually have some form of conflict but I don't agree that a hierarchical structure is the only way to resolve said conflict. You could just as easily apply any of the methods of governance that humanity has devised to resolve a conflict so I don't think the method of governance is crucial to the resolution of conflict. I think that getting both parties to agree to a satisfactory resolution is what is critical. That can be done with force as in a hierarchy where an external party enforces a resolution on both conflicting parties or it could be done without outside intervention, this obviously happens all the time in a variety of situations.
Ideally, every conflict should be able to be resolved directly by the people involved without additional harm being caused. Maybe there is a way through education or other tools that we can build that would allow people to resolve any conflict in such a manner? Maybe prevention is the best remedy and there exists a way to defuse conflict before it reaches a level that cannot be easily resolved. My point is that resorting to authority or force is not the only solution.