I think that makes certain assumptions about how Zora engages with the world, which may or may not be correct. I'd really like to rewatch "Calypso" as it's been ages, but Paramount+ seems to have...misplaced the Short Treks in my country.
The whole reason they came to the future was that Discovery's computer couldn't be disabled or removed after merging with the Sphere data and becoming Zora. So (she?) is always online and conscious. She spent almost a thousand years alone before Craft's arrival. At the time, I could have accepted some disaster that forced the crew to evacuate (or killed them all) and Discovery became lost, with a final order to hold position. But for Starfleet to intentionally put the ship (from which Zora cannot be separated) in deep space and abandon it, I cannot interpret as anything except cruelty.
What I'm trying to say is, I don't think it can be called cruelty if Zora, in her capacity as an artificial intelligence, doesn't mind. It may not be accurate to assume she will react in the way a human would.
Clearly, adherence to duty is important to Zora. She was ordered to remain in position and so she did. Nothing indicates that she didn't mind, only that her sense of duty outweighed whatever her feelings were. I read her interactions with Craft as belying incredible loneliness.
Ultimately, Zora's feelings are beside the point. Starfleet condemned a sentient being to (at least) a thousand years of loneliness. We do not see them consult Zora about her feelings on the assignment. She is simply ordered to do it. She is given no conditions on which the order terminates. She might still be there, still alone, a million years after Craft's departure. That's why it's cruel. It's cruel to give such an order. And, as a further twist of the knife, the instrument of that cruelty was Michael Burnham, ostensibly Zora's friend. "We had a good ride, but I'm old now and Starfleet just doesn't need you anymore. Rather than give you freedom to go and do you please, we'll order you to stay in this place indefinitely, alone."