There will never be a change to the behavior in CS6. It is now "feature complete" and any futher development is going to happen only for CC versions.
Your only hope is some third-party developer is just as annoyed and thinks he can find a way to do it via plugin or script, but I wouldn't hold my breath waiting at this point.
That's sad. That they would strip useful features and add useless "features" is incomprehensible to me. They're going the route of Quark, I remember when InDesign was the "Quark Killer" and we were all like "what? no way". And then Quark went down a misguided marketing path and Adobe capitalized. Maybe Adobe hired all the Quark marketing people. We can only hope there's an "InDesign Killer" being written right now since Adobe has lost touch with people who actually use their products professionally.
Features that you and I find useless may not be for others, and it's pretty much assured that a large number of users asked for and use the new features in CS6.
I have seen fetures removed that I found very useful (the navigator, for one), but I think the behavior with links was unintended and simply missed in testing.
Have you tried just checking the Search for Missing Links in This Folder option without doing anything else?