Presumably the optimal size for survival when humans aren't applying pressure via fishing is bigger. Perhaps "ruining" is hyperbolic, but this is making the fish less fit for their environment.
Their environment is one where humans prey on them, especially on the large ones. It's a selection pressure like any other and becoming smaller on average makes them more fit for that environment.
It is making them less fit for their environment? I can see how it is making them less fit for the environment they used to be in before they were subject to large scale human fishing, but that's not their environment now.
If that’s the case it should return if we stopped fishing.
Not always the case. Any number of things can happen that could prevent that from happening, like extinction, as an extreme example.
No. A certain gene expression can just be gone forever. Nothing guarantees the desired expression will evolve again.
Sure it does, there is still variation in the sizing of them. If the previous size was the ideal one, and assuming that has otherwise not changed, the larger cod will be more fit and breed more.