I think the problem is not hierarchy but unquestioned authority. And this authority then leads in consequence to a hierarchical and flawed systems.
There is for example nothing wrong when companies internally use a hierarchical structure or a baboon tribe does that. In both cases there is no unwarranted trust placed into the leaders. The company has to compete on the free markets and the baboon leader is constantly challenged by rivals.
But we trust our government and these power structures are not under pressure. We believe their stories and follow their laws. This is what makes it possible to get a deeply corrupted and hierarchical structure that is never found in nature and that is also very unstable.