It seems the writers did not adequately explain the purpose of an Ion pod, or more importantly, why it had to be jettisoned in order to save the ship.
I have no problem with that aspect of the story. Screen time is limited, and it's not necessary to explain everything
for the sake of suspension of disbelief. Even Kirk brushes off the explanation as common knowledge, "Everyone here in this court knows the dangers involved."
I simply took the situation at face value—what was done was necessary, though risky, and involved split-second timing. Opening "ports" in a firewall is also necessary, yet increases risk.