Welcome to the forums
Glad to see the problem's already dealt with, but I don't understand exactly what you mean by "but I didn't unbind the gamepad button from that command, since it wouldn't let me."
This should work regardless of whether you have a gamepad plugged in or whatever:
1) Open Settings Window
2) Click Controls button
3) Click Abilities
4) Next to Use Ability 2 (may need to go to the next page of the tab for this, I forget), click the Edit button
5) Left-click the button showing the joystick binding.
6) Now that it's waiting for you to press the new button you want it bound to, right-click to set it to "None" (I think some of them ask you to press Escape for "bind to none" but I don't think this is one of them).
At what point does that process break down (for, say, Ability 3 since you already fixed Ability 2)?
Thanks