Wouldn't an AI ship - something like the Romulan drone ship in ENT just with an AI in place of a telepath - be just an glorified probe?
Or a capable combatant, at least for very short engagements. I'm specifically thinking of "The Battle" where Picard single-handedly flies a cruiser into battle. Removing even that single "hand" looks very doable in that episode... But Starfleet could alternately assign a lone humanoid operator to each of its massive starships to keep guard over the apparently untrustworthy AIs.
Of course, a full crew would be a nice thing to have for repairs and maintenance. But the very fact that the ships can make do without a crew for a while can be used as evidence that there are fairly advanced artificial thinking processes available, and these can in emergencies or special situations replace the live crew easily enough.