More information has been added to this smear on the New Kadampa Truth site, so we are including it below.
Truth: In 1996, Fifteen abbots and teachers from Sera Je Monastery wrote an open letter against Geshe Gyatso, excluded him from the community of the monastery and named him an “apostate”. The reason for this action was Geshe Kelsang’s outspoken criticism against the Dalai Lama’s ban of Dorje Shugden.
James Belither, who was NKT Secretary at that time, said:
“The campaign to discredit Geshe Kelsang is clearly an attempt to silence him and to act as a warning to others. As one Tibetan Lama living in America said to another Lama living in Germany who was planning to come out publicly against the Dalai Lama’s ban ‘No, you mustn’t do that. They’ll do to you what they’ve done to Geshe Kelsang.’ “
What does it mean to be ‘expelled’ from an institution you used to study at? It doesn’t take away your years of study and meditation or diminish your spiritual qualifications at all. From this we can see that the expulsion is merely a political action and an empty gesture.
The August 22 1996 “Declaration of Expulsion of Kelsang Gyatso from Sera Je Monastery” reads in part:
“… These days, [in Kelsang Gyatso] the demonic cloud of overwhelming arrogance displays itself with a mass of deluded pride, like a bat who thinks he is above the sky…. This demon with broken commitments…. burns with the flame of unbearable spite towards the unsurpassed omniscient 14th Dalai Lama, the only staff of life of religious people in Tibet, whose activities and kindness are equal to the sky.”
This was not the only abusive, politically motivated letter received by Geshe Kelsang for his opposition to the Dalai Lama’s ban on the practice of Dorje Shugden. Throughout the summer of 1996, leading up to his “expulsion”, he received a constant stream of angry letters. Examples include:
From the Freedom Movement, Youth Congress, Tibetan Women’s Association and representatives of the Three Provinces Movement:
“… you are doomed life after life… telling others not to keep pictures of the Dalai Lama reveals that, although you wear the mask of a religious practitioner, in reality you are the running dog of China and Taiwan. Therefore, we the Tibetan people both inside and outside Tibet will unitedly stand against you as a source of harm to the spiritual and temporal affairs of Tibetans.”
From Tibetans in Dharamsala to “All the followers of Geshe Kelsang Gyatso”, August 20th:
“It is also a well-known fact that due to a slight disagreement on views with His Holiness the Dalai Lama, you had banned portraits of His Holiness in your business-oriented Dharma centers. This insane and demeanous (sic) act had caused disgrace to the Tibetans as a whole and is no better than the savageous acts of the Red Chinese. We, the six million Tibetans, solemnly denounce this ill-acts…. On keen examination over your wrong doings we have concluded that it is impossible for a jaundice-stricken person wearing the mask of Dharma to be a true Buddhist Geshe.”
(For a refutation of the smear about not putting up the Dalai Lama’s pictures, see here.)
From Tibetan Community, Kathmandu, Nepal:
“We feel called upon ourselves to let you know of certain facts about him so that his impudent ravings do not lead astray well-meaning followers of the path…. Your “guru” has the misguided audacity to challenge the omniscience of the Compassionate One to the utter disgust of us all.”
Because of a number of abusive, obscene and threatening letters, and because of warnings from Tibetan friends, since that summer Geshe Kelsang has to live in a location known only to a very few people and to have tight security whenever he is teaching. It is in this political context that he was “expelled” from his monastery and stripped of his Geshe degree. In reality, he is one of the best-educated and most qualified Geshes alive today.
This situation and the letter speak for themselves. Geshe Kelsang was always regarded highly by his peers at Sera Je, and while in Tibet and India was acting fully within the activities of the Gelugpa tradition. He did not receive any censure or criticism from within the Gelugpa community until 1996, when the Dalai Lama implemented his ban on Dorje Shugden. At that time Geshe Kelsang publicly stated what was already well-known in many circles in Tibet: that the Dalai Lama’s main motivation for the ban was to unite the four schools into one so that he could become their sole spiritual leader.
The letter from Sera Je makes numerous false claims, such as that he was a “chronic tuberculosis patient”, and has only one main accusation: they claim that (a) the Dalai Lama is Geshe Kelsang’s root Guru, and that (b) by disobeying the Dalai Lama, he is breaking the commitment to rely upon his Spiritual Guide. As a consequence, they claim that he should be expelled from the monastery. Geshe Kelsang has explained clearly that the Dalai Lama was never his Spiritual Guide, and never received any empowerments or even teachings from him. He has also explained that in order to rely sincerely upon his Spiritual Guide, Trijang Rinpoche, he would never be able to follow the Dalai Lama’s ban on Dorje Shugden. Geshe Kelsang’s behavior is in fact the opposite of what is claimed in the expulsion letter.
Finally, on a related note, Geshe Kelsang cannot be excommunicated from the Gelug tradition because it is not a club; Gelugpas are those who follow the teachings of Je Tsongkhapa, and Geshe Kelsang has devoted his life to upholding and propagating those teachings.
See also the refutation on the smear that Geshe Kelsang is a ‘self-styled Geshe’.
New Kadampa Truth Blog 
For many years now, thousands and thousands of Kadampa students have been denied free and normal contact with their venerable Dharma Teacher, Geshe Kelsang, due to the violent threats from fanatical followers of the Dalai Lama. It is just like a Buddhist “fatwa” and completely outside the values we Westerners cherish.
I can remember, back in the mid-1990’s the sense of shock and frustration felt that our precious Dharma teacher would probably have to live in hiding for the rest of his life due to this. After many years of free access to our guru, now that was a thing of the past. It was then that I started to understand the power of politicians such as the Dalai Lama and Kalon Samdhong manipulating people’s fears for their own ends, using religion for worldly purposes.
This has been a great shame brought on Buddhism by these political manoeuverings within the Tibetan form of Buddhism – principally by people blindly following the 14th Dalai Lama’s wishes. Thankfully the New Kadampa Tradition has now been registered as an entirely independent Buddhist tradition within English law and gradually will become free from all such interference.
The main reason why NKT-IKBU chose to do this was because they recognized all these problems such as this one experienced by Geshe Kelsang and his students were the result of mixing Dharma and politics – with higher lamas such as these ones using the holy Dharma for political aims.
It is ironic that the Dalai Lama, renowned as a champion of religious freedom, has – in his own back-yard and now worldwide – stomped on the religious freedoms of millions of people in a very brutal and heartless manner.
As with all forms of repression and dictatorial structures it is only a matter of time before they collapse and people rediscover their original freedoms. The activities of the Western Shugden Society bringing this repression out into the world’s attention is a part of this historic shift. In future people will view the last 370yrs of the poisonous mixture of religion and politics within Tibetan Buddhism as an aberration only corrected in the early part of the 21st Century due to the Dharma coming West.
This is so incredibly sad and a sure sign of our degenerate times. It is also our collective karma as NKT practitioners to experience this. All we can do is purify our mind through our Guru’s continuous blessings of pure Dharma wisdom and hence repay his immeasurable kindness.