The Judge does appear to have them on a technical point in the CWA that appears to be written to cover navigable waterways. These streams are generally about 1 to 2 feet across...not even big enough for a toy boat.
HOWEVER...if the quote of the author of the article is correct...and the revised rules allow for the dumping of mine waste...then you are correct in saying that this is a very bad thing.
The practice of moving the overburden and then replacing it is the practice that has been going on all along. We have a Judge stretching the CWA to challenge the legality of permitting.
So you contend that its been illegal all along...I contend that it hasn't been...though the Judge would like to think it has been...but can only challenge on a jurisdictional basis...and on the qualifier of fill only being allowed for "constructive purpose".
But...I'll grant you being horrified at the "just dirt" comment in hindsight...as there does seem to be some question of whether it is simply overburden being discussed.