Since bucks darken quicker than hens, I would keep a comparatively darker buck. I definitely wouldn't keep it if it was both dark and had fungus growing on it. I will not keep a hen, hatchery or wild, if she's spitting roe, no matter how bright she is. That's just my own policy. Also, rivers like the Queets have plenty of spawned-out chrome nate hens that fight like hell. I've seen guys conk these hens, with the reasoning that if they fought so well, they must still have some fat left in 'em. Please release these fish, as they have the potential to be return spawners. Run timing is another factor to consider. I've kept many dark bronze spring and summer kings from my namesake river. Everyone of these has succulent meat. But, I won't keep a bronze fall king from the same system - yuck! The bottom line, I guess, is to observe the condition of the fish when it comes in. If it's totally black, but is still well proportioned and firm; try keeping it.
In regards to the second part of your question; I don't think we can totally prevent it. Maybe plant "early" returners that will not return with the bulk of the native run, like the situation on the Bogey. But in this instance, the weakest part of the native run, the early natives, get pounded on by the proverbial "meat-hunters." It's too bad that recreational management paradigms haven't accounted for this facet of native populations. Anyway, from the perspective of many, hatchery plants is better than no hatchery plants.