Exactly right!
One more thing, all what these pump need to protect the f*g fish is a screen or a cage around the suction pipe(s). Any contractor can put a stainless mesh deep in the soil and higher than the highest possible water level around the pump suction inlet piping, et voila!
The only thing is that environmental whackos don't want a solution; they want control, pure and simple.
I have other non-engineering suggestions that couldn't be put in writing.
Same thing I was thinking, but on a larger scale since the intakes are so huge. Screens close to the intake would probably restrict flow too much, so you need a containment area for “de-minnowed” water. Something like a large reservoir/basin that keeps the minnow or any other wildlife from getting anywhere near the intakes constructed around the intakes to provide enough volume for them while protecting the precious little minnow.