I resided at Sera monastery for a total of about 20 months from 2003-2006. From 2004 onwards I had a basic enough understanding of Tibetan to know what was going on. My teacher was selected by HHDL to serve as Abbot and held that position for 10 years, partly because of his ability to handle the Shugden issue.
At first, the Sera monastery administration tried a "live and let live approach", where the Shugden monks could do prayers in Pomra khangtsen but those of us who didn't want to participate didn't have to. And during the kangso pujas very few monks attended unless they were financially destitute and needed the money. I would say there were only about 90-120 monks who sincerely believed in the practice, out of a khangtsen of at least 400. Things came to a head because the Shugden supporters pushed the issue, handing out copies of the prayer to all monks during pujas and pressuring them to recite. Hanging large Shugden thangkhas in the khangtsen, and fining those Pomra monks who did not attend puja.
Because of this situation, my teacher and the administration at Sera Mey felt they had no choice but to draft the oath for monks to sign. But this was after extensive discussion with HHDL and patiently waiting to see if the Shugden people would lighten up. After they tied up a visiting Dharamsala politician to a chair, the situation was sealed. Khen Rinpochey felt Shugden had to be controlled into the monastery, for the future of the lineage. I doubt any of the protestors have visited the monasteries of South India in the past ten years so really the information they are receiving is not first hand, but rather hearsay. It is simply an opportunity, I feel, for those who have grudges against His Holiness the Dalai Lama to try to damage his image.
The khangtsen was also being torn apart by the dispute because a new shrine hall was being built and the Shugden elements wanted a protector chapel in the back, and planned on ordering large statues. This further aggravated the situation. Once again, not from the side of the abbot and HHDL's supporters, but from the Shugden side who kept trying to push the issue. The harmony of such a large monastery (Jey and Mey combined form Sera, which has about 5,000 monks) is essential and the Shugden situation was becoming out of control. Not only were threats being made but there were arguments between monks and a deep feeling of disharmony.
In addition, some of those practicing Shugden were even attending high tantra initiations with HHDL despite the fact that HH stated that to do so would harm the lineage, his life etc... In short, they were taking HHDL as vajra master but deciding not to follow his direction in practice. When I asked one monk whom I knew supported Shugden why he was attending an initiation HH was granting in India, he told me to shut up and mind my own business. I was later warned by friends to be less open about my disapproval for such matters because people had been previously physically harmed.
So, that is pretty much all the information I have to share. Of course it is my experience and the experience of my teacher. But, because I stayed at Sera for a reasonable period and speak decent colloquial Tibetan, I feel I am better qualified to inform people about what is going on rather than NKT cadres who have never set foot in India. I doubt even GKG has been there in the past decade.