To a large extent I agree with you. But it's also true that nuclear submarines have a reputation as being among the highest-stress and most dangerous postings in the navy; there is far less room for error than with a non-nuclear or surface ship. Carriers, the other major nuclear ship type, have much larger crews and lots of space per person in comparison with subs. Which is why it has taken so long to reach this point.
It's not as easy as "everyone just needs to get along", it's "everyone needs to work together professionally and we cannot afford any mistakes". Besides, it's just as stereotypical to assume the men are boors as it is to assume the women are helpless. The reality is not so much that men are boors as that putting people in close proximity and under stress pushes people to the limit - nuclear subs are famous for this - and adding women to the mix makes it undeniably more complicated for everyone.
Again, I am by no means against it. But it's simplistic to think it's something we can "just do", just like that. We need to come up with a system that works, and we don't have it in place yet. The pilot program linked by the OP is probably designed to identify issues regarding mixed-gender crews, to help develop future rules and so forth.
If you read memoirs by submariners from WWII onwards, you get a sense of just how claustrophobic sub duty is, and the issues with having mixed crews become immediately obvious. I'm not saying they're insurmountable, but it's not easy either.
To think that neither women or men can handle a change even under such conditions is a bit of an insult to our forces isn't it? We have men and women serving together in actual combat scenarios with their lives directly on the line, somehow I think we can manage close quarters.