Governments suck, nothing new under the sun.
The basis of the ruling is kind of funny. Article 24 of the Japanese constitution says this:
> Marriage shall be based only on the mutual consent of both sexes and it shall be maintained through mutual cooperation with the equal rights of husband and wife as a basis.
Despite the article saying "shall be based only on," (in Japanese: 両性の合意のみに基いて成立し), the judge argued that same-sex marriage did not violate this article because if the marriage doesn't contain "both sexes" or a "husband or wife" in the first place, the article implicitly cannot apply to them.
As a result, this also seems to mean that same-sex marriages in Japan don't require the consent of both parties (though realistically, any prosecutor can likely find another legal basis to act upon any crimes this might appear to enable.)