A spiritual practitioner should be focusing on spiritual practice, not wordly thing like the independence of a country. The welfare they are concerned is the spiritual welfare not social welfare.
What does gaining independence bring to a spiritual practitioner? So that they can practise in their 'home'? If so, does 'home' bring them faster to enlightenment? I remembered Atisha studied Boddhicitta in Indonesia, not in his home country and he was attained after 12 years of study.
I do not think Dorje Shugden practitioners create the division among Tibetans, it was until HHDL imposed the ban Tibetan people started to separate themselves between the 2 groups and monks were forced to give up the practice by the government. It has never happened in our modern world that a government put their failure onto a group of spiritual practitioners and spend so much time and effort to suppress them instead of making improvement on the welfare of their people such as education, medical, etc.
Now, every Vajrayana practitioner should know Guru Devotion is the most important element to gain attainment. Unless it was an instruction from the guru, otherwise we do not give up a practice passed down to us from our guru. HHDL is not the guru to everyone in the monastery, he is not the guru to every Tibetan. At the spiritual level, his instruction to give up DS practice does not have to be followed at all, this does not mean he is not respected. At the secular level, all Tibetans including monks should listen to him, that I agree.
So I do not think Shar Ganden and Serpom Monastery are heading to the wrong way. They do this because they are devoted to their Guru, they are keeping the practice given by their gurus no matter what happens. They did not hurt others in the process of separating themselves, they did not say bad things about other people, they did not use violence to make their stance. They choose to be separated so that they can do their practice in peace.