Great story, had no heard it before. It occurred in the general area of the contested territory of Kashmir. India and Pakistan have had numerous clashes here, some have even speculated if a nuclear exchange is to occur in the future, it could develop over Kashmir. So is there any question recon drones would be in this area? Pakistani? Indian? Chinese? US?
The article considered drones, but only fixed wing drones. They did not consider rotor wing drones that can hover and also fly both vertically and laterally. Those three flight characteristics can account for the observations of the scientists (geologists, not aero engineers or even physicists.) A drone flying laterally at ground level could be interpreted as moving on the ground when seen from a distance, for example.
What I don't know is the state of drone technology in 2005. We would not be talking about a hobbyist drone, it would have to have been at least commercial quality, if not military grade. It also would have been large enough for the scientists to see at a distance, and to carry the video and transmitting/receiving equipment necessary to make it a reconnaissance asset. There is also the question of range, both in terms of distances able to be flown and telemetry for command/control. Did such a drone exist 20+ years ago?
If I had to guess, I'd say this was an Indian drone the scientists were not supposed to have seen. The Indian government would prefer the world thinks there was a UFO, as opposed to the world, the Pakis and Chinese in particular, know they had that drone capability.