With respect, I feel your post contains some misunderstandings about the NKT. It's not true that the NKT is 'isolationist' because Geshe Kelsang and his students have been rejected by certain Tibetan Buddhist Teachers and traditions. For example, when the NKT joined the Network of Buddhist Organizations (NBO), many Tibetan Buddhist groups chose to leave because NKT was admitted. This is clearly sectarianism, but it is generally the NKT that is accused of as being sectarian.
The main reason why NKT is isolated, if you want to think of it in that way, is because of the Dorje Shugden issue. The Dalai Lama has ostracised all those who are practising this Deity, including the NKT. Many of the Dalai Lama's followers are indeed angry that Geshe Kelsang has opposed the Dalai Lama on this issue, but it's one of free speech and religious freedom. The Dalai Lama's reasons for banning this centuries-old Deity practice are weak at best and wrong at worst, but that's another issue! It's a perplexing matter, but it's caused a lot of animosity and bad feeling in the Tibetan Buddhist world. Arguably, if the Dalai Lama hadn't rejected the practice in 1976 and banned it in 1996, there wouldn't be a problem between NKT and Tibetan Buddhist organizations these days, so who is really responsible for the schism that has developed in the Buddhist world?
Je Pabongkhapa was neither 'corrupted nor destroyed'. There is ample evidence from his life story that he was the living Buddha Heruka. What happened is that some lamas, due to jealousy about his power and popularity as a Teacher, began to spread rumours about him destroying Nyingma monasteries and so forth. Je Pabongkhapa himself is completely blameless. As it says in his biography on Wikipedia, he disliked politics, but unfortunately some Tibetan lamas do use Dharma for political purposes, and this is the cause of this misinformation about Je Pabongkhapa's life. Politics is always the root of division in issues such as this and the Dorje Shugden problem.
In your comments regardingthe statement by Amnesty International regarding the persecution of Dorje Shugden practitioners, you say:
The decision was that although the Dalai Lama had perhaps suppressed religious freedom and acted unwisely with regard to followers of the deity involved, no violence had been committed against them whereas it was clear that the followers of that deity had committed acts of violence and perhaps assassination.
No such statement was made by AI. Rather, they said that they could not become involved in a debate regarding spiritual matters. All the AI statement says is
None of the material AI has received contains evidence of abuses which fall within Al's mandate for action — such as grave violations of fundamental human rights including torture, the death penalty, extra-judicial executions, arbitrary detention or imprisonment, or unfair trials.
In other words, because Dorje Shugden practitioners have not been tortured or imprisoned, complaints of restriction of religious freedom and human rights are not severe enough to fall under their remit. You will notice that they do not deny that such abuses have taken place, nor have their said (as implied by your words) ' it was clear that the followers of that deity had committed acts of violence and perhaps assassination.'
Please don't put words into Amnesty International's 'mouth' that castigate Dorje Shugden practitioners inaccurately. Thank you.
The text is here:
All the best.