As for bypassing the clutch, I think everyone is thinking into it a little bit too much. Not that I do, but if I did install one on a manual, I would simply bridge the starter output from the remote starter and connect it to the switch side of the clutch switch. Thus when the vehicle is cranking, it is also bypassing the clutch. Both are (+) polarity, so it would be simple. Then you retain the stock clutch in to start feature.
To make the remote start safer on the manual, you can use a pair of mercury switches. These are installed parallel on your shifter, and send a ground (-) signal if they are in any other position than neutral. You must be sure your remote start unit has a (-) wait to start input, usually used for diesel's wait to start light.
It is not a safe thing to do on a manual, because the car will roll. You can however make it less of a threat. There are too many variables to say that something will not go bad. Remeber, most remote starters try to crank 3 times before they shut down. So there you are, chasing your car down the street, youve almost caught up to it....you go to open the door to stop it..... then......that mother fucker cranks again. The chase is on.