Overstay with Spouse Visa question

If you dont like Japan. You have choices.

I cannot imagine how someone not married, having no child and from "2nd or 3thrd zone" countries would be treated if they forgot to extend their residence card....
Immigration law (this kind of rules are not called like this in Japan though) and all that are not international social welfare.
If people from abroad tend to work illegally or to take advantage of marriage status, these can be good reasons to make rules strict.

First of all, consider you were expected to know all the rules about your situation. You are not a passport holder of Japan. It means you are expected to go through certain processes, always. It's no one else's fault you lack in management skill on your situation.

the immigration will get systems allowing different processes based on different cases...they will not
They treated you quite generously, based on your case.

In Europe 2 persons from different countries (still one being a national the country where all reside) and having a child will not be separated....you know
I have different information than you have, but I don't think it's cruel or anything.