She didn't treat Jon well, but what that got to do with what happened. Jon Snow is not her child, not even her step child really.
To Cat, Jon was just someone who could have one day rivaled Rob for Winterfell. Bastards cause a lot of problems for some noble houses.
to be honest I couldnt stand the bitch from the jump based on how she treated Jon. But a few episodes back when speaking to Robb's wife she explained how she thought it was all her fault once she broke her promise to the 7 to accept Jon. It was nice to see how she had a conscience when dealing with him but in the end she couldnt help herself.
Just thought it was ironic that her favorite is dead and the only potential heir to the Stark name is the one she treated like shit