There are usually alarms on the market that are made to remote start a 5 speed.
Clifford Solaris and a few others are made for that, you have to keep the car running, exit, arm the alarm, and the alarm will shut the car off and remember the shut down state. Basically it knows the car isn't in gear so it will start it if you tell it to. If you use a standard alarm, you're on your own. I don't know what's on the market right now, but I know there have been models in the past that will do this safely.