Chaff launcher is a gimbled weapon counter measure. It does nothing to missiles.
For missiles you have two options:
1. Point Defence Turrets(PDT) - which fires at objects such as missiles, torpedoes and limpets.
2. Electronic Counter Measures(ECM) - which releases a pulse that will disable missiles, torpedoes and limpets in small radius around the ship. It is almost unusable.
Once a homing missile is locked and fired upon ship it will chase you until it expires. Nothing breaks the lock. You have options to disable with ECM or give the time for PDT to destroy it. If there are a lot of targets, PDT is quite inefficient.
Alternatively you can target the missile/torpedo and shoot it down with weapons or even lock and fire a homing missile on it.