Personally I think that it would be counter-productive to remove this entry now, I think the best course of action would be improving the entry to remove the controversial parts (what you already mentioned doing it yourself), and as nobody argued against the intention of the post, I think it would be nice to start up an official blog where we can put up these kind of posts in the future.
I think the very existence of this message is controversial in the sense that we don’t have anything similar to this message on www.php.net. I think removing it and putting a clear removal message instead, with pointers to what phpng is makes the most sense. FWIW, I am arguing against the intention of the post in the sense that it uses www.php.net to ‘fight’ misinformation on news sites. That can be done on Twitter, blogs, or comment sections. As I think you pointed out, we never did it before, not when people wrote the ‘fractal of bad design’ and not when PHP was accused of being insecure. In that latter case, which was all the rage back in 2006, I used my own blog to fight this misconception, not www.php.net. Zeev