I have a couple of secondary NPC which for different small reasons become hostile to me. In one case I just got a bottle of bier which I didn't realize was considered as stealing, and the guy unsheathed the sword and attacked me.

Is there any way to make those NPC again non-hostile ? thanks

You have to kill them, it shouldn't get you a bounty if they strike first.

well, killing them was not exactly my idea of having them not anymore hostile

Have you tried putting your weapon away? If you didn't draw your weapon, draw it and then sheath it again.