Why did he take the potion?

[PerfectBlue]

From what I can gather from the game, I take it Daniel had taken the Amnesia potion so he could kill Alexander without all the side knowledge of what he had done with him.

(Killing the little girl and other people).

Is this correct, or am I missing something?

Yes he took the potion so he could focus on that, because he was haunted by his own actions. The turning point for Daniel is when he murdered the innocent girl and could no longer justify his actions.