That latest raw update also shows supported devices. The EOS-1Ds is still shown as supported by Mountain Lion in the knowledge base article that accompanies it. Bump!
I wonder if using Disk Utility and verify/fix permissions may restore your RAW capability.
Don't have Aperture or Lightroom.
I installed the recent raw updates into 10.8.2. The DB5W2360.TIF file has a generic Preview icon. Graphic Converter 8.3.1 opens .cr2 files, and it opened this TIF file nicely as well. GC is willing to modify white balance with a condition that it cannot be done in place, and must be exported to a different format.
Not much help, I know.
Take a look at Darktable. Non-destructive raw, 32b/channel open source alternative to Lightroom. Has OS X port available, though principal development platform is Linux. The 1Ds is supported on Linux, and possibly on OS X too. Do not believe this cares about Apple raw support, as it is likely BYOB, BYOdriver.
This may have possibilities for your raw file support on your 1Ds.
Also, take note that connecting a camera to OS X apparently launches a PTPCamera process that blocks Darktable. They offer either killing this process, then running Darktable, or provide a link to an automated solution.