You were a good friend to lend him a sympathetic non-judgmental ear. I'd like to offer my explanation as to why he was crying.

This has to do with psychological frames, people's goals, and the Overton Window. All three together work together to present an interface between an individual and reality. Most people struggle to fit the path of their goals through both their own frames and their Overton Window at the same time, and therefore tend not to notice those aspects of reality which exist outside their frame, Window, and goal path (rather like a horse with blinders on). Consensus with others as well as reference to demonstrable reality are two of the ways which people develop this interface.

Sometimes reality will present demonstrable evidence which does not fit AT ALL in the frame/Window/goal path, like the UFOs in AZ your friend saw. This causes the frame to collapse, and the Window and goal path reevaluated (evidence of an affair is a common example of this). When this happens to a person, they tend to follow a phenomenon similar to those grief stages in their efforts to try to establish a new frame by which to build a new Window and goal path.

The problem your friend is facing is building a new interface with reality which incorporates this experience of his. Your lack of forcing him in the direction that others most likely have tried to force him is what resulted in the cathartic reaction.

In essence, his experience tells him he is not crazy, yet the consensus point of view conclusion would tend to lead to that conclusion. That's a conclusion he would prefer not to come to and your unwillingness to come to that conclusion was an extreme relief to him.

IMO, you done good. I thank you for your kindness to him. I hope at least some of my explanation makes sense to you.