I’ve always assumed it’s because Gus knows that Victor was seen at the house (the house where Gale Boetticher was murdered by Jesse Pinkman) — remember that Victor and Mike had a conversation about the fact that he’d been seen (Mike was upset at it, and Victor didn’t think it was that big of a deal). Gus isn’t one to leave any possibility that he could be discovered by Victor’s carelessness, so he knows it has to be done.

Of course, he does it in the way that he does as a power play, hoping that the shock of it will convince Walt and Jesse to fall in line (i.e. “Hey guys, if I’m willing to kill my trusted assistant because he screwed up, do you really think I won’t do it to you if it comes to that?”)