The BEPs were alright for a contemporary act, I guess, but very out of place with who the halftime acts have been since 2005- music legends/royalty. Of those legends to play since 2005, Madonna probably holds the most relevance in terms of capturing widespread public interest (globally, of course it's no contest).
If Madonna were performing between the years of 1985-1994, the NFL would have cause for concern, in regards to what she may do. But while she's had her moments in recent times, she's nowhere near as button-pushing in her work as she once was- and I'm sure the NFL spoke to her about such things.