Well, there's always the power of the purse strings. This is the power which makes the legal age to purchase alcohol 21 throughout most of the United States, and for a time imposed maximum speed limits. These are limits that would normally be established by individual states, and the homogeneity was achieved via the purse strings. In each case Congress passed laws1,2 saying that a state would only receive certain federal fundings for interstates and highways provided they had laws that adhered to these limits.
The basic Supreme Court precedent on such matters is that these laws are legal so long as they meet the following criteria:
- The spending must promote "the general welfare."
- The condition must be unambiguous.
- The condition should relate "to the federal interest in particular national projects or programs."
- The condition imposed on the states must not, in itself, be unconstitutional.
- The condition must not be coercive.
As such, if Congress can find some substantive matter of funding which is related to female genital mutilation (FGM), and passes a law that provides certain funds only if FGM is banned by the states, and this law is deemed by the courts to adhere to these standards, then they may achieve a de facto Federal ban on the practice. However, there is no guarantee every state would adhere to the condition.
It is not immediately clear to me what such a matter is and how to construct such a law, but as you were only interested in knowing the available powers, I won't try to figure that out.
1. National Minimum Drinking Age Act
2. National Maximum Speed Law (repealed in 1995)