Charlotte should have won because she's the one heading into the title match at WM. Unless you're adding Bianca to the match, Charlotte kind of has to win that.
But she certainly should have struggled more and had a cheap or lucky win instead of no sell, powerup, clean and decisive win, followed by a post-match beat down. That does nothing to help Bianca and not only hurts Bianca, but the whole NXT women's division looks weaker when a main roster talent comes in and smashes one of the top stars. For all the old school, classic NWA mark booking that HHH loves, that's not the kind of shyt that ever would have happened with Ric Flair doing a guest spot in a territory against a top star. He would have either lost by count out/DQ/stoppage to set up a rematch, or won by count out/dq/stoppage/cheap win to keep the territory's star looking strong for a rematch or when he's there next week when Flair is on to another area.
Now, there's still room for Bianca to get revenge, win the ladder match at Takeover, get inserted into the WM match, or challenge post WM. Typical WWE booking will have this be the end of Bianca's part of the story and people get mad about it and boo the Rhea/Charlotte match at WM, though.