The ban is troubling indeed. Why does the Dalai Lama, the world emissary of peace, harmony and tolerance instigates such a ban on his own people, against his own teachers? Why?
This is what I think:
While dealing with samsara, we most often must choose between two evils, simply because it is samsara.
Just as when the Buddha, in the Jataka tales, resolved to the killing of a sea captain so as to save lives and save the sea captain from heavy negative karmic actions.
With higher vows, such as the peerless Bodhicitta vows, benefiting others may take several shapes that may be mis-understood by some.
The bodhicitta vows reflect a mode of thought and action specific to a Budddha.
When a Buddha act, it is ALWAYS for the benefit of others and with clairvoyance.
Does the Dalai Lama's mind have the qualities of a Buddha's mind?
Hard for me to say, who am I to qualify the Dalai Lama?
But with inferential logic, I can conclude that it is likely.
If the Dalai Lama is a Buddha, then he has clairvoyance, he has wisdom, he has compassion, pure, complete wise compassion, therefore he has the skills to do what is most beneficial.
His direct students that follow his instructions of not practicing Dorje Shugden do create merit on that ground, on the ground of following one's root Guru's instructions. How otherwise?
Those that go overboard however may have different results...
Long term, we will benefit, and I say this even without having to understand the why, how etc....
I say it with the faith that His Holiness is Chenrezig, if only because my own root Guru says so.