Gary,
I have not seen the article but your account is horrifying.Acid/sulphate problems are well known on the east coast rivers and receive publicity from time to time. I have not seen reports about the Murray before but I presume they must have been known to geologists and river hydrologists for a while. I guess other problems of the river have masked this one.As you say the one obvious solution is not available. Did the Author have any other remediation to suggest?

"The problem can be prevented by raising the water level to reinundate banks. But there is no water to do this."

Yes there is.
There is water.
It is just not being allocated to the environmental needs of the river.

There has been a massive fish kill in northern NSW which is being attributed to oxygen depletion resulting from flooding. There's a fairly consistent history of fish kills due to chemical run off during flood times in southern Qld and northern NSW, but that part of the story usually comes out later on when nobody's paying attention.

Some of the floodwater will eventually get down into the basin. It may or may not be enough to get the Murray moving again, but even if it does get there, what condition will it be in after the accumulated garbage of a decade of drought reaches the basin?

We've sweltered here in southern Qld for the past 3 days with humidity of what feels like about 5000 percent and only light showers, but the medium range forecast is for a month of either rain or showers. Same goes for northern NSW. With any luck there'll be sufficient volume getting downstream to properly flush at least parts of the Murray.

Water allocation then becomes an even more interesting question. If the fish kills are caused by oxygen depletion the water should be reasonably reoxygenated by the time it gets halfway down NSW. Of course, that would be a better plan if more of the natural ecology (reeds, fallen trees etc) had been left alone to do their job. If, however, the kills are evenly partly due to runoff, you'd have to be mad to want it by the time it gets where water is most needed.

If, as has so often happened in the past, the water is toxic sludge by the time it gets there, the problems will be compounded. And cotton farming seemed such a good idea at the time (sarcasm alert).

The other problem with relying on water from up here to replenish the rivers downstream is the disruption to vertical distributions of temperature, oxygen and nutrients which, if the inflows are fast enough, can kill a waterway as fast as toxicity by killing the organisms that keep the water both habitable and consumable. The Murray needs the weather to reorganise itself and start moving south.

I lived in Berri for a while a few years ago. At the time there seemed to be a large amount of retirees buying houseboats and living along the river. It was an alternative to the traditional Grey nomad caravaners. I guess the days of the Happy house boaters has gone.
I would expect that you will get rain there at some stage just like we have had major rain here and in NSW. I hope it doesn't come too late though. When is too late?