I don't think there is another murder committe by Walt in the show's run where the reasons for the killing are not quite clear. I sure hope someone asks Vince about this.
Interesting; like I said I thought the "why" was quite clear. Why did Walt go back to Albuquerque? Because he thought he'd come up with a way to provide for his family. Lydia was a fearful, almost paranoid individual with ready connections to killers, no compunctions about using them, and a lot of motivation to do so. Going to the lengths he went to with the money but not addressing that very real, life-or-death threat doesn't seem very likely for thorough old Walt.