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."