1. i think his first instinct was that he(Jon) is an honorable dude who has taken his oath to heart, and to have someone disobeying a direct order from the Commander of the Night's Watch means that someone must pay the punishment for dishonoring and disobeying their vow.

2. i think that once dude started sniveling and saying he was wrong and that he'd do it, Jon saw a weak ass dude who he couldn't trust in general, let alone have commanding a fort.

3. i think there was a bit of ego in it. Snow needed to flex some power in his new role to let cats know he's to be respected.