How to get a mac to wait longer for external disk to wake up upon resuming from sleep?
There are various google results for ejecting volumes on sleep, which should solve this problem.
First, write yourself a shell script to eject the volume. You could avoid setuid bits by using apple script.
#!/usr/bin/osascript
tell application "Finder" to eject (disks where name = "VOLUME")
Next, install the SleepWatcher tool and configure ~/.sleep or /etc/rc.sleep appropriately.
There are similar directions for remounting the disk on wake in that Mac OS X Hints entry, but maybe you don't need that.