In my country for long there were no such problems because the government imposed the proihibition of fisherman to go out to get some kinds of species during their mating and growing time. That way fish was allowed to reproduce and grow. Every time the fish you're eating has eggs a few dozens of new fishes could have been spared if the reproduction was allowed to take place. Also sometimes the nets used to catch the fish are too tight not allowing baby fishes to get out.

The problem with the law was that it was in reality imposing a time of starvation every year to the fishermans and their families, while the same species could be bought at the markets imported from other countries. The measure was one of the first to be abandoned when the political regime changed.

I don't really know what is the possibility of fishing companies to cycle between the fishing species during the year to let the other species grow, but that still seems like an alternative to me.

I also think that a fish diet is much more healthy than a meat diet, so a danger like the possible extinction of fishing species shouldn't be taken lightly just because we can get the proteins somewhere else.