And we come full circle on this issue. Japan has a pedophelia issue, plain and simple. It stems from a cultural emphasis on putting innocence on a pedestal. If anything can link Miyazaki to "moe" at all, it's that he also puts a high emphasis on innocence in his work. That said, it's one thing to emphasize innocence, but in Japan it has often been taken far beyond that to the point where innocence became sexually attractive. Hence, grown women often giggle and act "cutesy" because that is seen as attractive. It's not hard to see from there how "moe" and pedophelia came to be prominent. While it is perhaps most visible among otaku due to "moe" anime and manga, it is much more widespread. Miyazaki's frustration is really at Japanese culture in general.
This whole thing is more a side effect of Japanese sexism than a cause, though, in my opinion. The roots to that run much deeper, I believe.