The advice not to evacuate the South Tower was not so unreasonable at first, when it was widely assumed that the first plane crash was an accident. There was no expectation that another plane was coming.
People outside were being killed from the first moments, by falling debris and burning jet fuel. In that situation, people were probably safer inside the South Tower than they would have been running around outside. And the police and fire fighters likely had their hands full dealing with the North Tower. Another horde of people evacuating would not have helped the situation.
Of course, hindsight is wonderful, and after the second plane, it became clear that early evacuation of the South Tower would have been better in this case. But I don't fault people who couldn't accurately predict the future, during 10 or 15 minutes of utter chaos.