I understand not being proud of one's own culture. Many of my foreign friends are like "American culture is so amazing!!!1!" and sometimes I feel like saying to them, "If only you knew all that has happened in the country's history."
Japan does have atrocities in her past. The culture is far from perfect. But that doesn't take away from the amazing, colorful uniqueness of your culture. When I visited Kyoto while I was an exchange student in Korea a million years ago, I was blown away by the beauty and the kindness shown to me. I was well aware of what was done by the Japanese during WWII and other things but that didn't color my experience.
Every culture has blemishes. I can't think of a country or culture that can claim it hasn't done something crappy. But each of them remains beautiful. I hope you can find some peace concerning your culture. Don't be so hard on yourself!