I don't know the exact details of these cases, but I think the comparison with Saudi Arabia and Russia is a bit over the top (even though I agree that the potential to stifle news reporting is a real one).
The Japanese judiciary isn't a branch of the royal family (like it is in Saudi Arabia) or under the direct influence of the supereme-leader-for-life (like it is in Russia). In the case of the love-affair, I don't know the particulars but my guess is the issue hinges on whether the information about the affair is, or should be, in the public circle. And, its probably a civil case, not a criminal one. And, the penalty is almost laughably small by any standard, so, again, it feels like hyperbole to compare it with Saudi Arabia.
The "quasi-rape" case I don't know anything about, but again it seems like its a case more about the defendant's right to privacy than it is about whether or not the rape occurred. Was the defendant a minor? Was there some need to protect his/her identity? I don't know, but it seems the case was more about exposing this person than it was about defending his/her actions. If Paolo provided more details we could dig a bit further.
The Sumo case mentioned in the article Thomas posted was something I dove a bit deeper into (a great way to practice Japanese, by the way). This case seemed really strange to me, but it, too, hinged on the issue of whether or not the issue of match-fixing was sufficiently proven at the time of the trial (2008), and the court decided it wasn't proven sufficiently. Then, later on, in 2011 or so, more details and evidence emerged, and the magazine and reporter were ultimately vindicated.