When it's your men it's an act of war. Your men, paid low class soldiers, are doing it under noble orders. For some realms, it could even be an honorable tradition.
When you dirty your own hands doing it, you are a criminal. Hey, the logic might be a bit screwy by modern standards, but it sounds alright for its time period. Besides, your judge can ban you for looting or fine you. And when you have at least five soldiers with you who have won the most recent battle, if any, a bunch of peasants sure won't be too keen to stop you. When they do they'll have numbers and be loosely organized as a giant mob. But they wouldn't be too eager to die piecemeal against your professional soldiers outside a warehouse.
When you're alone, the peasants know they stand a much better chance. This isn't a game like Assassin's Creed where you're a superhuman fighting machine. You can escape, yes, but sometimes you're surrounded. You can take out maybe even a dozen. Then how many more before your body feels tired?
Two things to keep in mind: Swords are heavy. Infiltrators specialize in stealth and ambush attacks, not sustained overt combat.
