soulblade64: Twice I've played through the game now and twice I've had Lavalette throw down his sword rather than fight him... why, because I've had no real incentive to play the game different from how I normally would.
If the different animated cutscene you're given and opportunity to meet Louisa La Valette are seriously not enough motivation to kill him, some stupid little popup that arbitrarily assigns worth to your actions will be equally meaningless.
There are also the two story branches in late Chapter 1 and mid-Chapter 3 that significantly alter the way events play out. If altered content, different cutscenes, and different abilities that you'll either obtain or miss out on (you won't get the "strong back" ability by killing Aryan, for example) aren't enough, then that's really a "you" problem rather than anything the game would be capable of addressing.