Keep in mind, this is a country where you are innocent until prooven guily. The cops don't get to legally go form hit squads and go shooting people they don't like. This isn't the 1800's.
I can certainly agree overwhelming force is not in general a good answer because it emphasizes and strengthens the belief the police are not to be trusted. Would you come out of a building someone was actively firing into? Surrounding the compound at Waco and firing into it was just dumb when dealing with a doomsday cult because it's just going to reinforce their beliefs.
The correct way to look at this tragedy is many police officers were previously soldiers, so keep in mind when they see a cult, their mindset is to kill or capture or dispense with extreme force and what you get is a whole lot of stupidity as compromise.