I'm not the person you replied to, but
of course people should respect Ye's name change. I expect in many cases it's simply laziness, though I do think there's some slack to be granted where a reporter may use "Ye, formerly known as Kanye West", because people may not know or understand what happened, and the point is to clarify. If a news source were to say "Elliot Page, formerly Ellen Page", I think that's fine too. (Only sorta related, but a while back Cardi B amused people, including me, by noting how much Donald Glover and Childish Gambino looked alike.)
Anyhoo, the Bee wasn't accidentally calling someone by the wrong name; they were intentionally doing it to bother the person, which is asshole behavior. It is also when people do it to Ye, and if the kid in your neighborhood had changed his name to from Karl to Brett, and some other kid always ran around saying, "Hey look, it's Karl. Where are you going, Karl?" I'd say that also qualifies as asshole behavior.
Even so, asshole behavior should be allowed, if discouraged. The problem is that the Bee was using their reach and audience to blast a specific trans person, publicly, with the goal of belittling and ostracizing all trans people, who generally already face harassment from society. This would be problematic beyond the simple question of manners whether the target is trans people, Kanye, or Brett.