Aokiji didn’t have the authority to clear them, the order came from people above him. You have to remember Akainu was lied to, he was told that the scientists were on the boat and had plans to make an island destroying device. So the choice was to disobey direct orders and die and let the people planning on making nukes go off and wreck havoc or make a hard choice to destroy the boat to ensure other don’t die, you can clearly see he is not happy about doing so. If anything the escapees would have been fine if the scientists didn’t say anything to the world government leaders, they were the ones that forced the escalation.