Yes, but not hierarchy for hierarchies sake. Organization via consent is fine and encouraged. The problem is when it's done by force in an attempt to justify the hierarchy.

You are correct. "Unjust hierarchies" is probably the term I should have used. Some hierchical structures are going to be necessary in certain settings. What's important is that they're non-exploitative and entered into with real consent from all parties.

Hierarchy by legitimacy is indeed a tough nut to crack. It works well when the organisation has a simple, measurable performance indicator, and when its micro economics are simple. Make widgets, sell widgets is a great model for this kind of structure but yeah, non profits are notoriously difficult to self govern.