Tolkien should be the highest authority on these subjects, absolutely, and I think this hierarchy of canon when there's contradiction is probably correct, as far as it goes. What we're talking about here, though, is an idea that entails rather hefty re-working of the legendarium, especially the chronology. And that work was simply never done. This is why I have such respect for Christopher Tolkien. He did the best he could with what his father left behind (if he hadn't it's unlikely we'd even have the grist for this conversation in the first place), knowing that he'd be the one taking the shots for any places where it just didn't measure up to the "finished" works.
So, to say that Tolkien grew unhappy with the idea that the orcs were originally twisted, corrupted elves is undoubtedly accurate. Unfortunately, any competing notions were destined to remain merely a gleam in the master's eye. When CT came to this section of the work, he looked at what was available, and decided that to go with any other version would mean that he'd basically have to go in and write all the background himself. It simply wasn't there. It's like if Tolkien suddenly decided, and wrote in a letter or diary or something that it would be more dramatic if Galadriel had worked for Morgoth in the First Age, but then repented and spent the Second and Third Ages atoning. And then died without ever doing anything more with the idea. It's intriguing, and deepens her character, giving her a much bigger role in what would become the Silmarillion... but it's just an idea that never got any follow through. If CT wants to put it in the Silmarillion, he's going to have to write the whole "Galadriel as servant of Morgoth" epic himself, start to finish. So, he passed on the idea. If that had happened, would we be in the forums here arguing that Galadriel used to be evil, Tolkien said so, exactly once, and never got a chance to change his mind again later due to death? I mean, Tolkien, if I recall correctly, never definitively decided how Galadriel even got back to Middle Earth in the first place. Do we want to have an argument that CT got that wrong too?
Orcs were bred from corrupted, twisted elves. That's what has to be the last word, because Tolkien never got to go back and make the necessary changes. Would he have done that, if he'd lived? Maybe. But it's like arguing about what Lincoln would have done in his second term if he'd lived. We know his intentions. We know the kind of person he was. But we can't know what would actually have happened if he'd lived. We'll never know. What we know, is that Orcs were bred from corrupted, twisted elves. Tolkien writing to a friend something like, "wouldn't it be funny if Frodo was secretly bringing the Ring to Sauron the whole time and Gollum managing to take it at the end is the only thing that stops Sauron from getting the Ring back? Re-writes start tomorrow!" just before he died doesn't and shouldn't have any impact on the story we already know. The people arguing the other side here are kind of using the George Lucas defense.