goes without saying that you have to be careful when you install remote start on a manual. the best thing to do would be to put a sensor on the shifter (below the center console) that would hook up to the clutch switch wire so that the car can only be started when the clutch is depressed or when it's in neutral. if you're really paranoid, install two neutral sensors, but if you installed it right, the chances of it failing are minute.
next, set the max crank time to the minimum it takes to start your car (minimum you can set it on aladdin 2000 is 2 seconds) so that if somehow you do remote start it in gear, it will only go so far before it stops.
lastly, get used to leaving your car in neutral and checking it every time you get out.
also, if you get the aladdin 2000 alarm/remote-start, and configure it for MT, it would be pretty much impossible to remote start it in gear. the way it works is you have to take the key out while the driver's door is still shut with your foot off the brake, it will keep the engine running (hence ensuring that it's in neutral), you step out, close all the doors, press ARM on the remote, it locks everything up and turns off the engine. If you open a door or disarm, it won't let you remote start it.
The only two ways you could remote start in gear is if you left the windows open, and reached in and put it gear without setting off the shock sensor. Else you'd have lock yourself in, put it in gear, and then remote start it from the inside.
that being said, aladdin's safety features can be annoying. I put a switch that turns them (the safety features) on or off. Normally I keep them on, but if for some reason I don't follow the procedure, I turn them off and double check that I left in neutral. I gotta put a neutral sensor in though.
As for your actual question: the easiest thing to do is to simply unplug the clutch sensor. Else you could figure out which of the two wires needs to be activated/grounded and use start-assist if you remote start has one. I just unplugged it.