Pinochet was a tin-pot dictator who ruled only through ruthlessness and fear of a knock on the door at night. Khan would be insulted to be compared to him.
Okay. Would he be correctly insulted, in your opinion? And if so, why?
He's not, really. The basic jist of Khan's original appearance was obviously that he was a ruthless, but nevertheless admirable-in -certain-respects, figure from history.You're also reading a lot in between the lines about Khan compared to on screen knowledge of him.
(You may nevertheless have a point about the trains running on time thing. This after all was the same show that had a Federation agent pervert a civilization into Nazism because it was the "most efficient state Earth ever knew." Which... yeah.)
Let's just ask Khan if he'd rather be associated with Pinochet or Caesar. Let's also ask Caesar if he'd consider Pinochet a peer.
To say someone was among the least ruthless of a ruthless bunch of tyrants is damning with faint praise.
No massacres under his rule is no guarantee there wouldn't be any if he deemed it necessary to maintain or increase power. (I'm sure Napoleon never believed he'd ever have to order the mass murdering of Haitians, but there he was.) As far as not attacking unless he was attacked goes, that could be strategic. Let the others bleed themselves dry, and then just mop up.