You can still run an aftermarket amp with the OEM stereo. If you buy an amp, you'll need some high level to RCA connectors unless you buy an amp with high level inputs. (High level = speaker wire, Low level = RCA jack) The OEM radio will still cut your bass output once you turn the volume knob past a certain point due to the processing unit in the radio. An aftermarket radio does not do this. You can buy a cheap radio with a 2 channel selectable RCA output that can change it from running a rear channel to a sub. This would give you front and rear speaker level outputs with a dedicated RCA output for your sub amp.
So buying a new head unit would solve the whole issue?