transferring all of their CH-53s over to the air force from the army
I think you've answered your own question there.
Fair enough, but if the RAF can transfer its entire Merlin force over to the RN then I can't see why it should be so difficult to do the same for the Chinook force and the army.
If it IS a deal breaker for the personnel, then you just retain the current air/ground crews under their current conditions (wearing blue uniforms but under a green command structure), and then when they naturally waste out of the force you replace them with army folk who I am sure would love the opportunity to operate the Chinook.
Not that difficult really.