i have a manual transmission in my car with the compustar remote start system installed by a well known car stereo shop in my town. and i don't have to worry about that one mistake because i've been driving manual transmissions for 9 years and i never leave the vehicle in gear when parked. i always use the emergency brake when i park it.
an auto start on a manual transmision is only as bad as the driver who doesn't pay attention to what they are doing. in my opinion if you know you wont leave it in gear then go for it. if you might leave it in gear then get yourself in the habit of leaving it out of gear everytime you park it. then get the remote start.
if you get the compustar and you already have the scion security in your car they will work together. my car shuts itself off, locks the doors, and sets the alarm for me. i don't have to do anything. its great i love it.
the compustar remote start will run you around 350 bucks. plus install. it also has other features like, turbo timer, valet, you can upgrade it to a two way remote so if someone is messing with your car or the alarm is going off the car will page you to come check out whats going on. its a really nice set up. well good luck.