Article is absolutely pointless without giving knowledge of his visa status. If he doesn't have legal entry into Japan, then he can't enter the country, even if he "has a life there."
It sounds like his Visa expired so he took a weekend trip to Korea to renew his 90-day tourist stay. This is illegal, despite that many people do this. I'm not going to jump to conclusions, but if he says he has a house and a girlfriend/boyfriend and he doesn't have permission for long term stay, that decreases his chances of entry. You should never hint at yourself returning for a long stay if you don't have an actual visa.
The steps to take would be to get a new work visa if possible, or summer working holiday visa, even. If not possible, go home to Canada, send his partner over and get married, then go back together on a spousal visa.
For those people saying "stay away from Japan," well I wouldn't expect every response to be intelligent, but you sound particularly ridiculous. I have had experiences with getting into Japan on shady visa situations, and everytime it's been straightforward and worked out just fine in the end. I even, stupidly, one time said "I'm looking for work" entering with a one-way ticket (the thing you never, ever say), and they asked me what I'd do if I couldn't find a job. I said I had money (no proof of this) and that I'd just go home if I couldn't find one. Entered fine.
This is a sensationalist article, it shouldn't surprise anyone if facts are muddled. For example he makes it clear that he isn't completely fluent but still quotes things the Japanese staff say as fact. He also makes some pretty big accusations - that he is being detained for writing scathing articles about TEPCO or the Japanese government.
I do have sympathy for him and I was outraged reading some of the things that I heard, guards trying to extort money, and the Asiana airlines employee as well. Especially the Asiana thing. I would be contacting that company immediately to inform them of what happened.
But as always, try to reserve rash judgments when you read one side of a story.