Get a Clifford Solaris, they are designed to remote start a manual tranny car. You keep the car running, get out, and arm the remote start option. The alarm does a diagnostic check (I'm in running, the e-brake is on, so I'm not in gear) and then shuts the car off. Then it's ready to remote start when you want it to. It's totally safe, and works great.
I have a friend (you know who you are) whose car ran through a fence because it lurched trying to remote start while in gear with a clutch bypass. That's not a safe thing to do..