If JK Rowling is a TERF, then it's likely that transgender people simply wouldn't exist in Hermione's universe.
IF SHE DID encounter one, though, she probably actually wouldn't end up being a TERF. HP takes place in the 90s, if I'm not mistaken, and her very white parents were VERY accepting of her being a witch and going off to wizarding school. So I think her upbringing, coupled with the discrimination she faces at school herself, would lend her to a more open and accepting mindset than usual.