I get what you're saying, but this is part of the mindset that allows billionaire CEOs to evade all accountability for their white-collar crime.
Sure, the judge arguably should reduce the jail sentence, but this is the law in Japan and prosecutors should pursue a penalty for contravening it, to discourage profiting off of unethical and illegal behaviour.
I get what you're saying, but the issue is that if the only punishment for a crime is a fine, then it is really just a service the rich can pay for. Even suppose you set the fine to be defined as the amount gained plus some extra. Most who commit the crime are unlikely to be caught. So you need the extra to be defined as many times the amount earned from the crime. But then you are unlikely to get the amount they fine, and might just make it so the person is more likely to commit crime to try to get out of the debt (see: world war 2 causes).
That being said, there are probably better options. Community service, restrictions on investing, etc. but those have their limits. Also, I don't know what Japanese prisons are like. They might serve a better function than the criminal factories of the US system.
I’m not gonna say this is karma biting him in the ass for disallowing the Sonic Xtreme devs use of the Nights engine, but I am gonna say that thinking about that gives me a very nice sense of Schadenfreude.