no it didn't disable it. what u have to do is go behind the glove dept. and then "rig" the wires so that it bypasses the amp. it's not that hard, just time consuming and frustrating trying to figure out the right wires. but beyond that, it's not too difficult.
or if you're going to install of the components that u have mentioned, then just forget about the stupid factory amp. just disconnect it if it makes u feel better. use a deck that has 3 preamp rca connections. 1 for subs, 1 for fronts, 1 for rears. use these to power all of your speakers. that should take care of it. good luck...