The situation as far as I can guess (that's the operative word) is this: Mathematica uses the Qt library for their interface. But in order to use the new version of Qt that supports Retina's high dpi, one has to compile the application using the Cocoa framework which has for long been the default application framework on Mac OS X anyway. Unfortunately, I don't think Mathematica does that. It uses the legacy Carbon framework. So in order to switch to the new Qt that supports Retina, they will probably have to rewrite a whole lot of front-end code.
By the way, this isn't just a display issue. The resolution of screen shots from Mathematica is also wrong. So if I paste a screen shot into Preview (a high-dpi application) and save it there, the result looks especially blurry when you embed it in a web page (or upload to StackExchange, for that matter). So I now try to avoid taking screen shots and instead use Export to PNG inside Mathematica. I also have a script that repairs the resolution for pasting into my Xemacs editor that I use to write web pages, but that's probably too specialized for this answer.