I remember my reaction after watching this episode for the first time: would Garak really be comfortable back on DS9 after having killed Starfleet personnel? Regardless of the circumstances, something like that does not go unnoticed by folks.
I have to assume that Sisko covered Garak's role up, in order to preserve a valuable future ally and save him from any retaliation among Starfleeters. I know they're supposed to be "evolved," but nobody's that evolved. There would be at least the risk of retaliation.
So doesn't this mean that Garak - being a Cardassian - already hates humans and secretly wants to kill them?
Sure, but that doesn't mean that in his right mind, he will act on those impulses. Garak's violent nature is what made him valuable to Sisko as the guy who can do the dirty work, and gave Sisko a motive to cover for him.