I'm sorry that this has happened to you. School can be stressful enough for some people, let alone having to worry about what others write about you.
Definitely, do NOT alter the letter. In some schools, this actually would be grounds for expulsion because you are falsifying documentation to gain acceptance to their school although I doubt that they would do so in this case.
My initial thoughts were rather different from others. Why did you choose this teacher? I aim to choose teachers that I know well and who I can trust will write me a great letter of recommendation. How well do you know her? Will she remember your paper about trans issues? If either of your responses are positive to those questions then I would approach her to discuss the letter because you have enough of a relationship to address the issue. If you just took one course and did well, aren't there other teachers you could ask? Regardless, whether you chat with this prof or another one about getting a letter, you need to address the issue with them in some way, shape, or form before you get your next letter from them so that things go more smoothly.
All the best, and good luck! let us know how it goes.