Well of course John confronts her. He is a scientist and a historian, he just has to know the truth. And honestly, where wouldn he run to? He is on an island, remember?
I also think he was really quick to catch on, even nowadays most people would need more time, brushing of the strange things cause they are just "impossible".
I love reading Fantasy and Sci-Fi, do I believe that those things really exist? No I don't, so I would search for other explanations until I run out of them.