Aren't we (as humans) finding out that picking on the smaller food chained critters, such as bait fish, is just as bad, if not worse?

Krill fishery - impacting the whale populations and everything else that depends on kill for their diets to survive.
Herring - impacting the Stellar Sealion populations, as well as the salmon/fish/birds.
Sardines - impacting many fish, birds, etc.
Anchovies - same, same.

I think we'd probably do more harm than good if we focused a majority of the harvesting on bait fish.

We tend to harvest fisheries in an all or nothing manner. The trend seems to be fish it until it collapses *then* work on recovering the fisheries.

Having no bait fish around because we are focusing fishing on them impacts many many aquatic species. Even I know that can't be good.