Yes, thousands of us have been lynched, burned alive, torn to pieces, beaten to death, and shot — just for not being cisgender. It happens every day.
In response to your second argument: Your vagina is not a gender — it is a body part. And it’s very much not the end of the story, unless you choose to willfully disregard volumes of published science. You can choose to stay in your ignorance, or you can educate yourself. That is your call.