Wow, sorry to hear this, hope everything works our for you.
Remote starts CAN be safe on MT cars, i've had one for 6-7 years now that I installed myself. I installed an older version of a Compustar alarm, however many companies make MT safe remotes starts. It works very simply too, here's some info taken from Compustars FAQ.
Quote:
I have a manual transmission. How do I set my vehicle up to remote start?
A: You have to set manual transmission reservation mode. Reservation mode involves leaving your gear in neutral. You must set your e-brake and a few seconds later remove the vehicle's key from the ignition. Your vehicle will remain running until you exit your vehicle and close all doors. The motor will shut down and your remote will receive a page back (2-Way remote) and lock and arm the system
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Basically, if you leave the car in gear, it stalls where it's parked when you get out of the car. However, I've never had this issue, as you know the cars running still, so you always put it in neutral.
Just some info in case you do want a remote start. If the car gets fixed, have the dealer remove yours and install a legit remote start. The Compustar (and others) even have smart phone apps that let you never have to use your remote again.