m4n8tpr8, I do know how this works. Media with biases cherry pick site specific info and conflates it with other generalized info to make things seem worse of better than an objective appraisal would show. The NYT article smacks of that.
Your post has a lot of "ifs" in it. How about some actual facts? What species were those 9 nests - common or rare or endangered? What were their specific distances from the launch pad? What were the actual damages to the various eggs - smashed, cracked, pushed out of nest, what?
More importantly, what was the effect on those or similar nests at similar distances due to launches after the water system was added to the launch pad? The first launch effects are not something that are planned to be repeated.
The truth is that restricted areas quickly get populated with all sorts of wildlife, basically because people are restricted from being there, so human disturbance is reduced if not eliminated. Some of the restricted areas near where I live are birding hot spots. And, birders get upset when they are denied access on some occasions. And, sometimes that even happens for environmental/ecological reasons, such as a rare, long-lived bird decides to nest there and the restrictions are actually to protect the birds from the birders, not to protect the main government function of that area. There is such a situation in-progress right now where I sometime went for hikes and nature photography.
From what I have read, SpaceX is trying to work with the government to pay for some other, nearby marshlands that will be preserved. If that works out, it is probably the best outcome for the wildlife, because it removes those areas from residential and resort type uses, which are far more devastating to ecosystems than SpaceX rocket launches.