Which is why I think the idea was that jettisoning the pod in the middle of the storm was the purpose of the whole exercise, and worth risking not just Finney's life, but all the 430 lives aboard. It's also strongly suggested that jettisoning the pod was always part of the plan: Kirk says "It has been suggested that I panicked on the bridge and jettisoned the ion pod prematurely", establishing the idea of a non-premature jettisoning.
There would have been a right time for jettisoning the pod, after Finney was done with whatever he was doing. That sounds to me like the pod was supposed to be launched, to a free-flying mission, even if the terminology sounds unusual. It's also possible the pod was supposed to be discarded after experiments were completed, but in that case there should have been no hurry: the ship was physically free to maneuver even with the pod attached.
Hmm that would account for having someone go in and prep it for launching.