JK isn't perpetuating any such beliefs. The beliefs that get people killed go something like this: "I hate you and therefore I want you to die and so I'm going to kill you".
Jk doesn't hate anyone and isn't calling for violence and doesn't want anyone dead.
Trans women are targeted and murdered at alarming rates as a result of hate crimes.
Perpetuating the stereotype that they are just aggressive men pretending to be women while innocently claiming it's all about feminism does feed into the mentality that gets trans women killed.
ETA, but I agree it's not her objective which is why I said it's a grey area. She inadvertently plays into the hate.