During 9/11, many people were told to go back to their offices. Order was maintained. I'm sure a "few" who went back to their offices died as a result. Maintaining order for the greater common good was the intent, whether or not order was actually maintained.
People who didn't evacuate will have died, but that doesn't make them sacrifices unless someone intended that they die. That seems unlikely to me.
Whether it's a subconscious decision or not, you may decide that it's better to maintain order and endanger a few people, rather than have everybody evacuate at once, cause chaos, and endanger EVERYBODY. Sacrifice a few for the greater common good. It's uncomfortable to fathom, but it's a real possibility, not a conspiracy and not evil either.
It's the numbers I don't get. If we need to evacuate 5000 people, are you suggesting it would go smoother if we told a few (eg, 100?) to stay in their office so the rest could get out quicker? Regardless of morality, I don't think that works. I doubt the evacuation would go smoother unless you told the majority to stay behind. In other words, the opposite of what you say.
Ordering a complete evacuation will probably harm a few people who get hurt in the rush, but that can be worth the risk if the threat is real. When the authorities did not order evacuation, because they did not think the threat was real, I think they accidentally endangered the majority to save that minority.