1. Leave the story unchanged
2. Publicly retract the story, but keep the text available with a disclaimer.
3. Publicly retract the story and "unpublish" it, i.e., remove the text from the website.
4. Silently unpublish the story.
Everyone agrees that #1 and #4 are very bad. ColanR is claiming that #2 is better than #3, and in particular that #3 conflicts with existing NPR policy. We are inferring NPR policy from an informal blog post, not some official document, which was written in the context of third parties requesting that content be taken down. However, it is quoting an AP Editor policy that is not in that context.
You can argue that NPR didn't intend to endorse this policy in the context when they were the ones who messed up, rather than it being a complaint involving a third party. But then it seems rather hypocritical.