The author considers "opting out of Wikipedia" a "nuclear option" that "often won't work". But there's nothing wrong with writing your own book/wiki about a specific topic.
Knowing that "the character of Kaworu Nagisa was originally a cat" is not going to increase your understanding of Evangelion. Would I wish for that specific piece of knowledge to be lost forever? No. But it would be much better served in a book/wiki dedicated to the minutiae of the series than in a general encyclopedia: it would be better targeted to a specific audience, and it wouldn't have the citation problems the author mentions here.
As a side note, the piece was written in 2013. Evangelion wikis are alive as well.
Not a problem per se, since Wiki allows referencing non-English sources. Of course, an English-language source is preferred whenever possible.