The ABL is meant to loiter near the launch site just outside of enemy airspace and engage when a launch is detected. During this time, you are right, there will be a massive heat signature. So the heat and the proximity to the target allow the ABL to track using radar and infrared.
But remember that this is just a single layer of a multi-layered missile defense system. The "ballistic" phase you described is meant to be countered by the GMD (Ground based mid-course defense), which includes the EKV (Exo-atmospheric kill vehicle). And you are right that a warhead is significantly harder to hit at this stage.