They actually covered this in the broadcast: Helicopters are faster to get the astronauts to medical, smoother in rough seas, and there's less risk of being swamped by a rogue wave. Plus, since the astronauts might have fatigue/muscle atrophy/whatever, it complicates potential boat transfers.
From the broadcast, they made it sound like a big factor is the 2 hour program requirement to get the crew out of the capsule. Maybe they can't reliably hit that mark with a well deck recovery?
[1] https://www3.nasa.gov/sites/default/files/files/orion-recove...