They didn't actually shut him down.
Thank you for posting this.
To explain a little further: a company is legally obligated to defend the trademark if they want to keep it. Nintendo wasn't defending their trademarks to be mean, they were doing it because they'd lose them, otherwise.
Of course, people grabbed the story and twisted into some "Nintendo bullying a charity by shutting it down" narrative. They'll probably continue to do so even after reading your post.
People love to get worked up over things. Even false narratives. Even speculation on hypothetical situations based on a thread of information. It feels a bit like it's getting worse, but I can't say for sure. My memory isn't that great =D
I describe myself as a little dose of toxic masculinity.