The best part of the holoship plan is the punchline: “In a few days, you're relocated on a similar planet without ever realising it.”yeah, as mentioned the holo-ship deception seems out of character for Starfleet, but it was necessitated by the assumption that the Baku were a low-tech, primitive culture. Also, it's possible that the higher-ups didn't know the EXACT plan for removal, they'd left the details to Dougherty, who'd devised the holo-ship plan with his Starfleet crew and the Son'a.
The Ba’ku never leave the confines of their village, never explore the local geography, and never look up. As farmers, they’re unaware of the local ecosystem. They’ll have no idea they’ve been moved until they start noticing the symptoms of aging.