How to get past your alarm system depends on what kind of alarm system your car has. Many remote start manufacturers sell addons for their modules to disable vehicle specific alarms, so perhaps that may be an option to look into.
To get the car to start you need: ACC wire to be hot, 1 or 2 ign wires to be hot (depends on car, mine has 2), and pulse the start wire to start the car.
You can get a frequency to voltage converter chip, have the FB read it to see if your car is started (reading a RPM value), and if so, stop cranking, same to see if the car is running.
Personally, I'd buy a cheap remote start that includes an AUX input, and use the fusion brain to trigger that aux input. If your computer were to say... freeze in the middle of starting, it would not shut off the starter (potentially causing damage).