Starfleet is not anarchist. There are admirals. There are federation laws and judges (1st directive, in strange new worlds, laws against eugenics). Those laws and positions of power are decided on a federal level. How do you do that in an anarchist organization?
I fail to see how a federation can not be a representative government (because different worlds have different political systems, representative democracy is the only one that can make them all on an equal footing).