I have absolutely no biological expertise on this whatsoever when it comes to our bay system and salt/brackish ecosystems or fisheries but in my experience with tailwater fisheries and drastic natural events like this one there is usually some upside that isn't immediately obvious... for example, a few years ago the Cumberland tailwater suffered a dramatic event due to repair work on the Wolf Creek dam. What had been a trophy trout fishery for 20-30 miles downstream was reduced to 10 miles or less due to the increase in temperature from the water coming from the dam upstream as the lake level continued to drop during the turbine repairs (which are still happening). The obvious downside was the impact to the trophy trout fishery, which not only affected the habitat size (reduced down to 10 or so miles from the dam) but also impacted quality as most of the larger fish downstream perished due to increased water temps.
The non-obvious upside to this is that it doubled the size of the striper fishery and, from what I hear, the stripers got fat and happy in the process - moving upstream munching on 20-30" browns and rainbows.
Aside from that, the increased water flow itself near the dam created some new spawning habitat for the trout themselves - time will tell if this really changes anything as far as trout fishing goes.
Bottom line is, there has to be an upside somewhere.... that's the way nature works (I think)....
(photo from my buddy Fred McClintock's page)