I'm not really sure what MSNBC was expecting. When you give a crazy person a TV show, you have to expect them to do crazy things. It's just that simple. Hand unfettered airtime to a person like Melissa Harris-Perry, and you should assume she'll end up using it to model her tampon earrings.
More importantly, if you let a person like Harris-Perry rant for a few years, she's going to end up with an ego the size of Manhattan Island. Since 2012, she was allowed to rant, rave, and flip out over all sort of imaginary racism, and the network said little or nothing. So it shouldn't really come as a surprise she finally decided that - in a world where everything was racist - her own network was racist too.