If your head unit has an internal amp (I am guessing it does), then you don't need the factory amp. You can just leave the amp where it sits and use an "amp bypass connector" to bypass it. That way, the powered signal will travel from your new HU back to the trunk, through the bypass connector, and then to the speakers through the factory speaker wiring.
Or you could remove the amp, but that rack is kind of difficult to remove. Also, it may start to squeak over bumps if you mess with it ... it's a very annoying squeak, trust me.