Question about Veronica Mars....?

Okay so there is something that has been bothering me. I think it is the finale of season 2, Aaron Echolls is in a hotel room and that Clarence security guy shoots him twice, then they show that Duncan ordered the killing. My question is, did Duncan have him killed because Aaron was let out of prison and he wanted justice for Lily? Or was Duncan trying to cover up his tracks? -- I know that they found evidence with Duncan's DNA or something on it, I think the award that was buried and found when the pool was getting dug out --