They're fine, but that doesn't answer the question:
Akane lifts up half the building and throws it. There's nobody inside; not a single person within what's left of your building.
During the freefall, people were being put in the building. The question is, why weren't they there when we landed? How did they get out and scattered among the rubble without being injured?The dust begins to settle a little more, and the sky begins to clear. You see civilians, mostly unharmed, and what injuries they have are minor at the worst. They're lined up across the ground, scattered slightly among the rubble.
It's possible Homura did the timestop-evac at the last second, like we were speculating on. It's also possible that Madoka wished them to safety. Regardless, though, something happened outside of our expectations.