As the article says, it diverts most of the flow during low-flow periods (i.e. summer) which means there would not be much left for fish passage. Might be fine, might not, I don't know enough about the ecosystem to say.
Additionally, there are some definite issues with sedimentation during construction. They excavated the channel to the intake and put all the dirt from the excavation into the stream for it to "carry away"[1]. This would not be allowed in most areas I know of - essentially, fish can't breathe if there's too much dirt in the water. Then several times it overflowed and eroded the channel - more sedimentation. The author even admitted using concrete liner would be the better choice, but opted not to because it was expensive - essentially, this externalized the cost of sedimentation to the ecosystem.
Diverting the water through pipes will definitely cause significant ecological change.
Nature minus humans endlessly causes the same sort of change, but to second an earlier comment this would be a nightmare to try to do in a lot of areas. In my area the most dire thing to touch is the flow of water -- with three layers of government/protection agencies monitoring it with a very close eye.
Your last two comments have been personal attacks, and we had to warn you about this before: https://news.ycombinator.com/item?id=18096897. If you continue to post like this to HN, we are going to ban you. I don't want to do that, so would you mind reviewing the site guidelines and taking the spirit of this site more to heart when posting here?
It's not primarily a moral or ethical thing. We're just trying to prevent this place from burning itself to the ground. That requires everyone to have a certain discipline with their angrier impulses here.
It might modify where the wetter parts of the area are, but I don't think that equates to destroying it.