I think it sounds like the person that wrote this doesn't really understand much about Buddhism; sometimes, yes, in history, some members of the Kagyu or the Nyingma have had trouble with the Gelugpa and vice versa (for example, see A Golden Swan in Turbulent Waters by Shamar Rinpoche, about the the life of the 10th Karmapa, contemporary of the 5th Dalai Lama).
It seemed to me like the article had both the Dalai Lama and Dorje Shugden pegged wrong--- this happens sometimes; there was an article in a local Virginia paper once after Shamar Rinpoche and some other Kagyus were erecting an enlightenment stupa; it was a very conservative part of Virginia, and they kept getting confused about what Rinpoche was doing; they seemed to find that the weapons that were put in there to pacify obstacles were there for some sort of militaristic reason (sorry--- tiny paper from Virginia 12 years ago-- don't have a link). This happens sometimes.y
I wouldn't say that Shugden followers are more conservative Gelugpas at all, and I certainly wouldn't say that we want the supremacy of our school over others. I would say that when the Dalai Lama wants to merge the tradtions all under him, that that is a supremacy of another sort; I think the Shugden follower just like to keep their tradition pure. Penor Rinpoche's Nyingmas always liked to keep to their tradition when I studied with them; in both cases they have a complete set of teachings that leads to full Buddhahood, so I think they just want to continue with the one that works for them so that they get to Buddhahood.