I agree with you, but I don't really think this problem is exclusive to Japan: I've met Americans in the past who hold some really, really weird ideas about Scottish people, and it worries me that this might be the general consensus in their country; but overall, as long as what they think is just daft and not hateful, I don't see it as a huge problem, more just a mild embarrassment on their part.
The internet being the internet, things often seem worse than they are because if you go looking for stuff to prove how weird people get over a specific subject you will find it. (Case in point: I once found an idol website for Philip Schofield, detailing absolutely everything he's ever done, with photos from the beginning of his career right up to present day and, if you know who he is, you'll understand just how fucking insane it is that anyone would care that much about Philip Schofield.)
I'm not saying that we should ignore or continue to perpetuate these stereotypes, at all, I just like to think these Japanophiles --despite being a particularly vocal crowd-- actually number in the minority, while most of us know that Japanese people aren't all perverts; just like Germans aren't all Nazis, Americans aren't all trigger-happy lunatics with a hard-on for war and, contrary to what the aforementioned American thought, Scottish people do, in fact, have electricity.