Yes but unlike say a democracy, you can't vote the theocracy out. You can't be treated fairly if you are not of the official religion. You become an outsider, never to be treated like a full citizen, because of who you are.

Imagine if instead of religion it was skin color, or gender, or hell even height - only people over 2 meters could be in government. Can we whitewash those too? Are they as legitimate as Theocracy? Why not?