Wait, are you saying the music is stored as separate audio tracks? That does indeed make it fairly easy – all you need to to is extract the audio tracks, speed them up, and put them back into the .bin image. (I thought you were referring to individual sound effects.)
There are several ways you could work around this problem, but TurboRip should get you started. (Yes, it's originally for PC Engine games, but all mixed-mode CDs work the same in the end.)http://www.ysutopia.net/forums/index.php?topic=69.0
Unfortunately, any kind of patch you make from this is ultimately going to contain the entire soundtrack from the CD.
I expect it ought to be possible to make a Python script or something to automate the whole extraction, re-sampling, and re-assembling process, but that would definitely take more time than I've got these days.