There are shinto believers in Russia and Italy!?I observe the Japanese use double standards. If person is Shinto, he/she is "cute and fun", and if person is Christian, he/she is "lazy and stupid". But as foreigner here, i actually find attitudes of Shinto and Christian Europeans quite similar. Well, Europe is also large..let`s narrow definition of Europeans to Italians and Russians i more or less familiar with.
Jenovah's Witnesses are tolerated, along with Mormons, in Korea primarily due to being able to learn English from them. But I suppose the situation is different for Japan.Well, one possible exclusion. Jehovah's Witnesses are treated in Japan with general hate, but also with respect to their capabilities and determination. If any Christian sect would succeed to convert Japan, i will bet on Jehovah's Witnesses.
All in all, what you said proves how Japan's perception of Christianity is deeper than mere social stigmatisation; the double standard shows as much. Therefore the problem may be harder for us to solve than we may expect.