It is known why the rivers are running orange. It is because the permafrost is thawing.
Sure, the exact, specific process causing the oxidation is being debated by scientists, but ... the reason is because the permafrost is thawing.
Anyway, what this nearly certainly means is that the artic has already blown past the feared warming tipping point and is now releasing methane, which is a much more potent greenhouse gas than CO2.
This article should be focusing on how this likely indicates that climate change will intensify faster than commonly understood by the general public.
It's more like the article is focusing on the wrong part of this story. The exact mechanism can be debated but we know what's happening and why: global warming. The article just doesn't want to acknowledge that so it focuses on the fact that science hasn't conclusively figured out the mechanism.
It would be like saying "the glass feel of the table, but we don't know why it hit the ground" just because we do not understand gravity in every way possible.
In mine closure, artic mines will protect their tailings and waste rock using thermal covers that insulate them from heat, and allow permafrost to form, thus entombing the PAG (Potentially acid generating material - acid drainage presents orange like this too). The frost prevent oxygen (and dissolved oxygen - from water) from interacting with the material, and causing the acid-generating reaction.
With the thawing of natural permafrost, iron that was frozen (as water soluble reduced iron) is released and then oxidized, causing the orange water.