I mean, the police usually stop a street fight regardless of who is in the right or who's wrong, mostly to protect the fighters and the people around them. If two (or more) aliens start fighting in a little town, crashing through buildings, and causing lots of damage, then the military doesn't have another choice but to aim at both troublemakers. Also, it's not that obvious to figure out who's the good or bad guy. At first glance, Faora and the others can be some sort of intergalactic police and Supes a criminal they're trying to apprehend. The general or commander stopped seeing Superman as a threat only when Supes saved him personally.