Female genital mutilation is a practice that confers no medical benefit to a woman, and can cause lifelong physical harm, and the federal or state governments can argue that banning it serves a rational secular purpose.
I personally feel that the ban on polygamy by the US Congress and Congress' insistence that the State of Utah MUST have a permanent non-removable ban on polygamy in its state constitution -- or else Congress can revoke Utah statehood -- was driven by animus towards the Mormon religion. If three consenting adults want to enter into a civil marriage (which is, essentially, a form of contract law), how is the State harmed? But, the SCOTUS of the 1890s found rational secular reasons to uphold the ban, and the SCOTUS of today wouldn't dream of overturning the ban, because of conservative Christian "family values".
I agree with Mr. Anchorduqoy's conclusion. With regard to contraception and abortion, we are favoring a conservative Christian viewpoint over all other religions.