Just to answer your questions:
1) yes it can work with only 1 throttle, in the setup menu you can specify only to use throttle 1 and not throttle 2.
2) I would indeed pull the reset on a fault detection, pull the reset (MCLR) to ground. This puts the chip in reset, a consequence of which being that all PWM outputs go to the 'off' state (so the complete power stage switches off). It does this very fast without software intervention. You may want to add something (flipflop) that keeps the chip in reset till you push a button to release it. You can also just reset it very short and allow it to start back up. In that case it will go through the normal startup, so first drive_0 where it will wait on throttle closed and/or motor standing still (dependent on what you enabled in the recovery menu).
3) every pin you don't use (including unused throttle inputs), I just leave them open
through that's not the way you're officially supposed to deal with open pins. What is always safe is to connect the pin with a 4700 Ohm resistor to ground. If the pin is an input it will just see a ground. If the pin is an output it can easily drive the load of 4700 Ohm so no harm is done....