Seems like you didn't read the article. His job was updating the website not modifying objects. Also, your argument is wrong on its face - the company he worked for modified objects to allow them to commit piracy. If you modify a stick into a shiv and stab someone, you won't be arrested because you "modified an object that you own" -- you'll be arrested because your modified object was then used in a crime.

Now, whether intellectual property laws are morally just, whether Nintendo are being assholes, whether he should be afforded free healthcare rather than having his income garnished to a private multi-billion dollar company, etc. are different issues