Because there is something called professional and human integrity. Own up to your mistakes. Accept responsibility. Do you force push a fix whenever you merge a buggy commit? I would hope not. I describe my mistake, and what I am doing to fix it. But what is done is done. Hiding it is just being unfaithful to your profession and in this case, to your audience.
The very first paragraph of the retraction notice:
> Editor's note on April 11, 2018: NPR has retracted the story that was previously on this page because it did not meet our standards. "Fairness" is one of our guiding principles, and to that end we have pledged to "make every effort to gather responses from those who are the subjects of criticism." In this instance, that did not happen.
So how does this not count as owning up to mistakes and accepting responsibility?
Your analogy with a git commit/`push --force` is flawed. In software, the end user is not at risk (without much deliberative effort) of running the buggy commit. In journalism, the article content is the actual end user product, and grievously erroneous content causes actual harm. Moreover, the mistakes that NPR admits to making were not just a "buggy" commit. It was the equivalent of checking in malware from the very first commit.