A theocracy poses too many problems. Aside from the obvious civil rights issues, it is rare that people agree exactly on religion. Even within the same sect or church there are differences of opinion and interpretation. It is a near impossible task to define how to run a theocracy given the vasts differences of opinion.
The motivations for theocracy are never justified, but they do and will occur. Given the nature--or expansive uncertainty--of peoples interactions with their life experiences, environment, and other people, religion and culture can have minuscule or gargantuan differences in opinion. Thus, a theocracy can never be fully motivated in a governing nation as it doesn't support the ideas of all its peoples. But really, what government ever does fully support all its citizens?