If an acceptable solution to you is having the drive not spin down in the first place, you can set than in System Preferences -> Energy Saver. Then you won't have to worry about it spinning up and halting the system.
I don't think you can change the behavior because it's not feasible for the system to guess when you'll need the drive available and when you won't. There might be SOME circumstances when you can be sure, but not in every case. For example: A dialog box comes up asking me where I want to store something. The system has no way to know that you'll NEVER want to store it on the sleeping disk, so it has to make the resource available (and refresh the system cache). Anytime the system needs to know what resources are available, it has to wake up sleeping devices. The solution is to not let your peripherals sleep when the computer is in use. Or else get used to waiting for them to wake up. You're probably not saving much power. Wear and tear is greater on disk drives that spin up and down than those that stay spinning. The system can't read your mind and anticipate exactly when it will need to wake something up.