Small note. The writer didn't choose the title, the editorial staff at the Boston Globe did. The person who actually wrote the article, Greg Beacham is a writer for the Associated Press, which syndicates their stories to papers worldwide. Those papers are then allowed to choose the headline they run with if they decide to run it. That's why he's included in the apology. He talked about it over on his Twitter.
So I have a hard time believing anything other than actual malice on the part of the Globe's editorial staff.
Quick search for "with prejudice" in the document. I guess they tried to argue that Meta was acting on behalf of the state when they "censored" their anti vaccine posts, but they failed spectacularly in doing so.