They used to make systems that would remote start the car as long as the transmission was in neutral. It came with a relay that sensed what position the shifter was in and would not allow the starter to engage unless it wasn't in gear. Maybe they don't make it anymore due to safety concerns...laws may have changed.
I remember years ago a guy I used to work with did one on his manual Civic. They put in a switch that he had to arm getting out of the car so that when he triggered the remote start it would work. Just a thought for you.