Is there some kind of script I can run to permanently turn them off? Preferably a zip file I can just flash in the recovery or something.
Easy, if your rooted download gscript and run one of these scripts one for of is lightsout.sh one for one is lightson.sh
push them to your sdcard/gscript folder then load them in gscript and run from gscript
there is allso trackballon and trackballoff if you want to turn your trackball on or off for some reason. I will have the green and orange led up later
NOTE: if there is an error like the lights turn off after a bit then edit the gscript lightson.sh and remove the line that says sleep1.
NOTE#2: this may cause soft reboots were your phone will run the boot animation and restart the xserver of android shell blah blah. nothing to worry about doesnt hurt your phone
If you are running a CyanogenMod ROM, there is a control for the automatic backlight that also lets you set the light levels fot when the softkey backlights go on (which you can set to 0 to never come on.) I don't have a CM ROM installed at the moment, but it's in settings->CyanogenMod ROM settings somewhere. if you cannot find it, I can dig around.
 I think it's in user interface->automatic backlight. That's where it was in CM6 (Froyo).
echo 0 > /sys/devices/i2c-0/0-0040/leds/button-backlight/brightness
chmod 444 /sys/devices/i2c-0/0-0040/leds/button-backlight/brightness