I decided I'd look into this tonight and actually it turns out it's very easy. The script took longer than figuring the mod itself. Surprise, surprise, the solution is in android.policy.jar again.
This mod will make pressing the volume keys wake the phone first, then subsequent presses will change volume as usual. I won't bother with a detailed how-to this time since I put some time into a fairly complete script, but for people who are curious, here are the details:
Method: private isWakeKeyWhenKeyguardShowing(I)Z
How: Delete cases 0x18 and 0x19 in the switch statement at the bottom of the method. These tell it to return true for volume up and down keys. Careful about changing the others. Some refer to non-existent buttons on the Atrix, but others (as I found out) affect your headset mic button and other events. For a detailed how-to on taking apart and putting together the android.policy.jar, please see this thread
The script is now universal, for all ROMs. OS X, Linux, Windows.
How does it do that? Like this:
1. It takes android.policy.jar directly from your phone.
2. Decompiles the jar.
3. Patches it.
4. Recompiles it.
5. Pushes the jar back onto your phone.
6. Cleans up and reboots the phone.
Some prerequisites before you run the script:
1. Obviously make sure you're backed up. You can't hard brick with this, but there is a possibility of soft brick if there's a bug. It should be safe because it checks for errors at nearly every command, but nevertheless have CWM ready. I have tested this on OS X and Windows. Linux users, you will need to test this yourself. It should be fine though, because you use the same script as OS X, but with a different adb. Just verify that the script and adb have the correct executable permissions, or chmod as necessary.
2. You must have java installed on your computer because it needs that to compile the android.policy.jar file. To check, you can type, "java" in a command line window. If you get a "no java command" type message, then java isn't installed correctly on your machine, or you need to add the path to java.exe to your path environment variable.
3. You must be deodexed.
4. Make sure to set your USB connection to "None" on your phone.
5. On your phone, go to Settings > Applications > Development and make sure USB debugging is turned on.
6. Plug your phone into your PC and let it install any necessary drivers. (OS X users ignore this, Linux users... You're on your own )
7. Then you can run wakeonvolume.sh for OS X/Linux and wakeonvolume.bat for windows.
* Thanks to natboy for solving the script issue for XP users!