At the risk of feeding a three-year-old troll...

This is ridiculous. Shinto is the religion of some 100 million people, and it's a lot more concerned with ritual purity than Emperor-worship. During WW2 even Buddhism was officially roped in as a form of Shinto... and if you think Buddhism is all peace, light and happiness, punch "sohei hiei" into your favorite search engine and read up on Japan's armies of warrior monks.

There's also the little practical point that shrines are, by and large, free to enter so boycotting them doesn't matter one jot. If you oppose the Japanese government's textbook certification process -- and note that there isn't just one textbook per course, but many approved ones that handle controversial issues differently -- then register your displeasure with the government and don't visit Japan at all.