What a huge cost they are paying in order to be popular with the Dalai Lama.
Indeed. Especially as many of them may not even have the Dalai Lama as one of their direct teachers. What is to be gained by currying favor with the Dalai Lama, when he is not even your root teacher? Is that to be held more precious and important than the samaya with our root teachers and our immediate lineage teachers?
Yes, Lama Zopa has told his students to discontinue the practice. He must have his own divine reasons for this, and students of Lama Zopa would do well to follow his advice. But there is a difference in following his advice and in disparaging other Lamas or others' advice. This isn't what Lama Zopa or Lama Yeshe would have wanted in the way students are treating other practitioners and practices, whether or not they did practice Dorje Shugden themselves.
Is it not "good" enough to just discontinue the practice yourself (as advised by Lama Zopa as your Guru) but remain quiet and respectful about what others choose to do? As you have also said, Vajratruth, these people could well have chosen to "remain neutral in the matter and let their own members decide for themselves."