Nothing in the dialogue mentions or even suggests "preparation". Got a quote?
I just choose to interpret the applicable bits the right way.
"We'll need somebody in the pod for readings."
Not for taking the readings, but to facilitate the getting of readings by priming the system.
"Report to pod for reading on ion plates."
Clearly, the futuristic act of "reading on" primes the plates.
"Finney here, Captain. Ion readings in progress."
But other systems still need priming.
"Make it fast, Ben. I may have to go to Red Alert."
And that marks the point where we deploy and run, ready or not. Note that Kirk does not
say anything even remotely like "I may have to jettison the pod".
Also, what was the pod going to do once jettisoned?
Study the storm, autonomously, with better odds of survival than a starship (and less at stake in case of failure) - while it lasts. Kirk was in a great hurry to get into the storm, suggesting it would evaporate or move away in a moment. Once that happens, they can go and look for the pod and get the results, physically or via telemetry. Standard tornado hunting stuff, that.
But, the episode made it clear that keeping the pod attached during an emergency would've destroyed the ship.
Nothing of the sort was ever stated. Instead, Kirk made clear that the storm was a threat to his ship, quite regardless of pods or other factors. And then he said that when the storm got worse still, he had to jettison the pod. Which is fully consistent with jettisoning being the climax of the mission, something Kirk was anxious to do because it would allow him to save his ship by sailing out of the storm
The very reason that Kirk is on trial is because he is being blamed for jettisoning the ion pod before an emergency.
Nope, he's on trial because Finney is dead, and evidence suggests both that Kirk didn't give Finney a warning necessary for his survival, and that Kirk had a motive to hold back the warning and cause Finney's death.
There was a full-blown emergency underway all the time, with various alert statuses to indicate it. That Kirk jettisoned before pressing Red Alert would be a poor handling of the emergencies at hand, and could be interpreted variously as incompetence or malice - but everybody knew he would
jettison sooner or later. That was assumed, inevitable, and no doubt the aim of the whole process.
Shaw is of course speaking out of her pretty ass: the ship was in danger already, per all witness statements. The ship suffered heavy damage, none of it ever attributed to the presence of the ion pod. But the prosecution would be motivated to use provocative expressions: Kirk looks more incompetent (or more damnably suspect) if he panics when there "is no emergency".
Spock: "It reports that the jettison button was pressed before the Red Alert."
Shaw: "In other words, it reports that Captain Kirk was reacting to an extreme emergency that did not then exist."
But of course it does not report that. It only reports that Captain Kirk did not believe in an extreme emergency yet, and thus didn't press the Red Alert button to express such belief.
Button pushes are the thing being judged in the trial. But button pushes do not relate to emergencies. Button pushes only relate to Kirk's assessment on whether there exists an emergency or not. If Kirk doesn't press Red Alert in time, Shaw can only accuse him of failing to notice or express that there is an emergency there; the emergency itself cannot be talked away by the silly woman.