The Gelugs were the most recent holders of power in Tibet and with power comes corruption. But anyone familiar with Tibetan history knows the other orders had their intrigues too, so it would be a little immature to dismiss an entire tradition and corpus of teachings because of unfortunate history. There were cases of lamas taking over eachother's monasteries even before the advent of the Gelug tradition.
There were huge fueds between the two palaces of the Sakya school, recent tension between Drukpa and Karma kagyu,with HH Gyalwang drukpa writing a letter saying henceforth his school would be known simply as drukpa. In Lord of the Dance Chagdud Rinpoche talks about power struggles and terma contoversies within the Nyingma.
I would go as far as saying you cannot find a significant Tibetan lineage with a history completely free of these things.
Phabonkhapa unfortunately left a
blight of sectarianism on the Gelug lineage but this is being remedied by hhdl and many other masters. They advocate fixing things, not abandoning an incredibly rich and profound tradition. True non sectarian masters see the benefit of studies in that tradition, Thrangu Rinpoche, tutor to hh karmapa, is a geshe lharampa for crying out loud, and Taklung matrul rinpoche also completed extensive gelug studies. We are talking about long years studying in the Gelug style. Obviously they feel due to the benefits past history can be forgiven, otherwise they wouldn't be there.
It works the other way too, Khenpo Jigme Phuntsok, Hh sakya trizin and HH Karmapa have all taught at sera, for example.
I have attended initiations of HHK with many Gyuto gelug monks participating.
My experience with Tibetans has shown me most are willing to put down theload of sectarianism, while the western white students seem to enjoy holding onto it. White converts like to beable to play the minority in their chosen religion. The most sectarian practitioners i have met are Westerners of the Nyingma and Gelug traditions, with about a 50/50 split. Most Tibetans I have met are eager to move on, with the exception of a few die hard fundamentalists who are increasingly seen as backward.
I findit weird Westerners not even born into this culture seem to want to hold on to past grudges from a feudal society. We need to move past this stuff if anyone in the West is to take Buddhism seriously. Otherwise we look just as clannish as the feuding sects of Christianity while we argue the sophistication of Buddhism. It is pretty sad, actually,
A foolish man proclaims his qualifications,
A wise man keeps them secret within.
A straw floats on the surface of water,
But a precious gem placed upon it sinks to the depths