Take debito's blog with a grain of salt as, even though is trying to do good things for foreigners in JApan, he tends to take it overboard and exagerates quite a bit and makes things seem worse than they actually are. I call him the Jesse Jackson/Al Sharpton of Japan.
I have more than 35 years experience with Japan including many years living there and have never come across even 20% of what he is writing about including run ins with the law of which I have had my share.
Sure, I have been turned down for an apartment here and there (but found one within a day or two) and even been refused admittance to certain bars and such, but it is rare and understandable to me although there are some who would gladly disagree with me. However, I have never been turned down for an Onsen or a hotel or a ryokan.
As with anyplace, including living in the US, you will find discrimination everywhere no matter what your race as I have experienced living in the Southern US. Although it is very rare, I have experienced it.
Just use the JREF search engine and you will find many posts about debito and racism/discrimination in Japan both positive and negative. I may be a rare case, but I have hardly experienced what many others claim they have experienced. However, it is there and always will be and one must understand that. However, it's what you make of it and how much you understand the Japanese mentality and their culture. For me, overall, it has been a positive experience while to others it has been a negative experience.
My suggestion is to go there and make up your own mind with first hand experience and do not believe everything you read on websites as there are many who have an agenda behind a thin veil of doing good, or what is right, for all foreigners residing in Japan