It can be done safely but you must understand the consequences if you do it wrong. The emergency brake can NOT be counted on to save you if you accidently leave the car in gear and then later attempt a remote start. Most professional installers will not do a remote start on a manual tranny due to the liability concerns. I love to tinker with electronics so I built a custom lockout using a proximity detector and a little ingenuity. Most people have had luck using magnetic reed switches to sense when the stick is in neutral and therefore prevent starting in gear.

My system uses a Keyance proximity detector to determine when the stick is in neutral. It is set up so there is no possible way to start the car without it either being in neutral or having the clutch depressed. As a backup failsafe measure I have two mercury tilt switches installed that will kill the motor if they sense forward or backward movement of the car. These switches also double as a anti-jacking device that triggers the alarm. I even went so far as to install a small two-color LED and an audible device reminder. When I go to park, I get a red LED and a soft warble tone to warn me that the stick has not be place in neutral when I'm exiting the vehicle. Bump the stick to neutral and the tone is silent and the LED glows green. Overkill probably but I liked the challenge.

If you do a search for the terms REED SWITCH and REMOTE START you'll probably find lots more info.