I'm not a body language expert, so I could never say with certainty what specific facial reactions during an interview mean or don't mean. Eye-blinking and throat swallowing can mean anything.
Based on the depth of the interaction between Meghan and the Fortune editor (and even the interaction between Meghan and the The *19th founder, Emily Ramshaw, and between Meghan and Gloria Steinem) the context and the actual content and give-and-take of such conversations, in my opinion, are the best indicators of a person's actual feelings and intentions.
In particular, Meghan referencing the words of Georgia O'Keefe, is very inspirational:
"I have already settled it for myself, so flattery and criticism go down the same drain, and I am quite free."
Meghan may want everyone to believe that she thinks this, but in my view she is very interested in what people think of her. She is engaged in a very deliberate media strategy to make sure people think well of her (and by default, Harry).