I am not sure where you are getting the guino power from, but you should be able to go straight to the battery and eliminate any chance of interference from the alternator kill switch.
And rest assured the guino does not lock up a metro with the cam signal kill switch. But an injector switch can "fool" it into giving false readings, or worse I imagine. I might try a 10k resistor across the switch/relay to hold the signal high but not give enough current to open the injector (assuming your switch is in-line with the injector). Obviously lots of creative ways to kill an engine
I can't cover them all.