Why did Gus kill Victor?

Two reasons -- he was spotted at the scene of Gale's murder and the police were looking for him, and to intimidate Walt and Jesse.

Maybe he didn't like him stepping outside of his role to try to cook. He did take it upon himself to do it. Meanwhile, he arguably didn't fully complete his job as muscle (Gail/gayle dies, Walter stays alive.
It also served as a lesson to EVERYbody in the room.