If you're really interested in the extent of the gov't's power to regulate in the area of religious practices, I suggest reading Church of the Lukumi Babalu Aye v. Hialeah, Employment Div. v. Smith and City of Boerne v. Flores. Three seminal cases in Free Exercise law. I'll chime in here, since I know the attorney who won the landmark decision in Boerne - the Supreme Ct. decision striking down RFRA (Religious Freedom Reformation Act), and I pretty much aggree with the logic of the decision.
You can believe anything you want. You think the supreme being is can of garbanzo beans, go ahead; worship a can of beans if thats your kick. The gov't can't legislate against beliefs. They can, however, legislate against action which may be a part of the religious ceremony or practice if such legislation is generally applicable and not intended to inhibit any particular sect or belief. Thus, the gov't can enforce criminal laws even if it interferes with the religious ceremony or practice, as long as the law wasn't directed at inhibiting the practice of that religion. Employment Div. was the famous case regarding the enforcement of a law forbiding drug use/possesion which was challenged by a group which used peyote as a part of their religious practice. Following Employment Div., Congress passed RFRA which was ultimately struck down by City of Boerne. As I recall, Church of the Lukumi Babalu Aye won because there the city wrote the law with the intent of inhibiting their religion.
So, if your religion directs you to engage in female circumcision (or male circumcision for that matter), go ahead, but be aware that if the gov't can find a generally applicable reason why such circumcision should be proscribed (say for example, public health reasons), they can outlaw that specific act. Of course, if the female objects and it is done forcibly, or without consent, it could well be prosecuted as criminal battery.