I'm not 100% sure, but to my knowledge, removing the stock radio should not give the car's factory alarm any problems. I do know of several cars(esp GM's) when you take out the factory radio, the car wont start, and alarm problems too. But i don't think you have anything to worry about. The stock radio has its own security, so if its stolen, it needs a entry code to power on. You should be ok to replace the stock radio with aftermarket.

13.5 @108 MPH-2.2 60ft(stupid FWD!)
S16G @ 18 PSI/FMIC/Running on MegaSquirt II (Now with sequential
fuel injection)
My webpage: http://eclipsed4evr.home.comcast.net
-1998 Mitsubishi Eclipse RS-T- "Toy"
-1992 Plymouth Laser Turbo AWD(SOLD)
-2000 Honda CR-V(daily)