The author isn't saying the problem is JSON. The same programming style exists quite a bit in older PHP code as well. This is because one of it's primary data

The author isn't saying the problem is JSON. The same programming style exists quite a bit in older PHP code as well. This is because one of it's primary data types is an list/hashtable hybrid. And JSON is similar -- it promotes those same structural types; the list and the hashtable (array and object, respectively). So programmers are using them, not just for building structures for data interchange, but for actual programming logic. The fix for the problem is just education.