Actually, I added a line right under it: ControlMap.addKeyToTriggerMapping c_PIMouseLook IDFKeyboard IDKey_RightCtrl 0 1
Basically making RightCtrl the "Secondary Control" for it. The reason for that is that I don't feel like reconfiguring my Joy2Key for flying (which specifies LeftCtrl). But that's just laziness on my part.
Anyway, it doesn't conflict with anything, since soldier movements/controls (prone) are separate from vehicle movements/controls (freelook).
If you don't feel comfortable, you can always back up the controls.con file before changing it and then revert back if you broke something.