Auto-attack doesn't stop a ship from firing on a target that flies into range, if my understanding is correct. All it prevents is the ship from automatically picking a target and going after it.
Regardless, even if the capital ship got the kills, if the Titan is below level 10, it will still share the XP with the capital regardless if it even touched the enemy. The only real way to reserve XP for the capital is to either get the Titan to level 10, where it will not be included when dividing XP after a kill, or to keep the Titan out of the gravity well.