Before the outrage bus hits 5th gear en-route to gullibletown, it's probably worth pointing out that there is little-to-no contextual accuracy to these news articles.
AM Hillier is appointed SRO for the Carrier ENABLED Power Projection Programme. The ships are just part of that Programme; along with F-35B when embarked, the CROWSNEST Merlin and a bunch of other helicopters such as AH-64 and Chinook. He heads the Programme. He isn't in charge of the ships. He has plenty of Maritime SQEP individuals working in the Programme to advise him.
This whole story is like someone getting upset at Sir Richard Branson for not being a Virgin Atlantic pilot.