I don't really understand how the fingerprinting campaign can be considered to be 'for the protection of the immigrant' whose prints are taken. The essential presumption is that foreign entries into a country have less of a connection to that country and are therefore more likely to abuse it; in this case, the specific justification offered seems to be combating terrorism. Which, by the way, isn't such an outlandish idea - regardless of the fact that Japan has not yet been attacked by foreign terrorists. But with regard to the law-breaking, whilst the notion might be intuitively true, generally speaking anyway, I am not sure how well it applies with specificity to Japan. I seem to recall somebody once linking to statistics which illustrated immigrants to be committing crimes at a proportionally lower rate than native Japanese?
Ultimately, the most glaring problem with regulations like this is the potential for abuse. As others have observed, mistakes can and do happen when matching fingerprints and people who've done nothing wrong can and do suddenly find themselves being unjustly dragged through some horror. However, the observation some people have made about being "treated like a criminal" holds, I think, only if being fingerprinted is usually associated in Japan with criminal activity. And even if it is, there are obviously examples of being fingerprinted there - say, for employment in a sensitive government sector - where no such connotation applies. What becomes important then is how the Japanese media decides to spin the issue; are gaijin or are gaijin not being portrayed as belonging to a criminal element while news of the fingerprinting / photographing campaign is reported on Japanese television.
With all of that said, I don't think I will have any objection to being printed and photographed and whatever else when I go. Whilst the "you have nothing to hide, so why object" argument is in my humble opinion a poor one, I just do not feel particularly threatened by this. I would be more worried about possibly reinforcing problematic social implications (gaijin = criminals) than about the occasional clerical mistake or the errant case of genuinely sadistic police work. And even along the lines of that worry, things like it being legal to be refused housing simply because of one's status as a foreigner seems like much more of a significant issue. No?
So with that, I shrug.
I should also probably admit up front that I wouldn't generally deign to protest or otherwise participate in a country's internal politics by any means other than simply leaving that country - voting with my feet, as they say - unless a) I had actually acquired naturalized citizenship, or b) I had married a Japanese citizen. But that's just me.