Not an alternative route so much, the posted workaround of disabling the vm applications folder in the dock didn't stop the dock from using up 100% CPU until after I trashed ~/Library/Preferences/.com.apple.dock.plist and used activity monitor to force quit the dock. mac mini, OS X 10.6.8, 2.66GHz Intel Core 2 Duo, 8 GB 1067 MHz DDR3. vm = Windows XP Professional, gave it 2 GB of memory I think. Or maybe 4, I might have been feeling generous.
I've also got a weird thing where my Windows application folder is full of duplicates, and pinning windows apps to the dock will create a ton of duplicates that are visible in finder but don't appear on the dock. But I fixed the 100% CPU thing at least...