Indeed, you need to get the Japanese culture completely and uncompromisingly to see what the schools here "teach" in a positive way. However the Japanese culture is about more than just submission and obedience, the other parts, I am fine with, but I am not going to leave my son in a system that considers imagination and critical thinking like deviance.
My parents lived in France for a while and still revere parts of French culture, so I'm familiar with it. Honestly I can't imagine having to reconcile that with Japanese culture. I'm often surprised, though, because French people in general seem to do well in Japan -- especially compared to Americans or British people. Anyway, I feel for your situation. It can't be easy. I hope you find a path that works out for you!
It is ridiculously easy to be a French in Japan. A lot of people immediately become very friendly to me when they learn where I am from.
Also, there's one thing I'll concede to Japanese culture: they do take food seriously here! That's also a strong shared point.
I can read your message and understand how you feel. Japan is a hard place to live in as a foreigner. The culture is not like a buffet. You can't take the bits you like and leave the other bits aside. This is especially challenging if you are raising kids, since the school system is going to instill Japanese values in your kids whether you like it or not. A few people have asked me if they should raise kids here and I think it's totally great, but only if you are ready to buy into the Japanese culture completely. If not, it's going to be -- as you put it: appalling.