TLDR; Gus Killed Victor because he let himself be seen at a murder scene.
Late in the series, Walter speculates that Gus slit his enforcer Victor's throat for "flying too high." I disagree with both the reason for Victor's death and his position in Gus's organization.
Victor's earliest appearance is during the flashback where Gus and Gail discuss Walter's product. During that meeting, Gail states that he'll be ready to begin production in a month.
Victor, who is holding the schedule of shipments, corrects him with two weeks. Twice, once with Walt and once with Jesse, Victor is shown acting as a purchaser, handling merchandise and distributing money. Next, consider that while Victor is always armed, he's never shown actually shooting anyone. Conversely, Mike, an actual enforcer, kills on-screen on numerous occasions.
Another important moment and the linchpin in why Victor had to die was the night of Gail's death. Mike presses him repeatedly to ask if he was seen. Victor confirms that he was seen and by several people. In fact, Mike is more concerned by the fact that Victor was seen than by anything that may have been in Gail's apartment. Mike is then the one to make the call to Gus and states, "Let's get this over with." before doing so. The moment in the show is played to mean Walt and Jesse's deaths. But I believe he meant Victor's. He was going to have to tell Gus that Victor was seen.
I believe the brutal nature of Victor's death was Gus venting his frustration. Mike draws his gun not to stop Gus or shoot Walt and Jesse, but to shoot Victor in case, Gus didn't kill him as efficiently as he did. Walter deprived Gus not only of Gail, who couldn't run the lab alone. But, Victor's own sloppiness deprived Gus of a valuable member of his organization AND Gail's lab partner since no one is shown being able to run the lab alone, forcing Gus to rely on Walt and Jesse. Instead of his preferred team of Gail and Victor, This is why there are now cameras in the lab. The strategies Gus used to replace Walt failed, and he had to fallback to monitoring him until other opportunities presented themselves.