There's no doubt whatsoever that Eriko's murder comes about as a result of prejudice against transgender people. We are told that Eriko had a stalker who started following her around after he spotted her on the street one day. Apparently, the man, who's described as “crazy,” liked what he saw and followed Eriko to her place of work at a gay bar.
However, the man initially believed that Eriko had always been a woman and not a man who had undergone gender reassignment. In other words, he didn't know she was transgender. But when he found out the truth, he was completely shocked. Not only that, he felt furious for, in his view, being made to look such a fool.
The implication here is that the man felt stupid for having developed an infatuation over someone he believed to have been a woman from birth, only to discover that, in actual fact, she used to be a man. This shows that the man is prejudiced towards transgender people; he's clearly not prepared or willing to accept Eriko for who she is. So he attacks and brutally stabs her. Eriko dies of her injuries, but not before she's beaten her attacker to death with a barbell. As Yuichi says, Eriko died fighting.