[... we didn’t want to shoot it down over land because the wreckage could have caused damage on the ground...] (paraphrasing)
But yet, there remains standing orders to shoot down ANY commercial airline that strays off course and doesn’t respond to commands.
They didn’t know it wasn’t weaponized or didn’t contain substances that could be airborne. I suspect that was the real reason. The area could have been cleared to avoid direct hits. No one knows what will happen with the next and next although obviously a shoot down is safer over unpopulated environments.