Can I replace my factory stereo with an after market stereo with out messing up the anti-theft system and or the cars computer system

I would like to replace my 2005 Chevrolet Malibu with a factory AM/FM Cd
player stereo in the dash, and passkey anti-theft system with an aftermarket
stereo.  I was told that if I attempt to replace the factory stereo that it will
cause the passkey anti-theft system to mess up due to the fact that it is
hooked up through the factory stereo and that it will cause the cars computer
to malfunction and leave my car unable to start or run properly.  So put
simply can I disconnect my factory stereo without causing any problems?