In practice cliques have the same benefits to agglomeration that e.g. corporations and proto-governments do. So freedom of association can’t exist in practice for very long, at least not freedom to associate with multiple effectively-equal cliques.

Cliques will certainly differ from one another and are likely to be unequal, much like “soft cliques” already exist today in larger cities. The question is more about how much power a clique should have and how exclusive and encompassing its membership should be, e.g., whether a person can belong to multiple cliques.