Yes, if we examine carefully, the issue is not about Shugden being a spirit or not, from the side of the Dalai Lama and the CTA and followers of the Dalai Lama. If it were really about Shugden as a spirit, then how is it the Bon faith is allowed and is even classified as the 5th School of Tibetan Buddhism? The Bon faith has its roots in spirit-belief /shamanism. We can still recall how Guru Rinpoche subdued the Bon spirits and converted them into unenlightened mundane Protectors.
If , in the spirit of religious freedom, the Bons are allowed, by the Dalai Lama, to practice their faith, then it stands to reason, that logically (even if the Dalai Lama truly believes that Dorje Shugden is a spirit), in the same spirit of freedom of worship, Shugden worshippers should be allowed to continue with their Shugden practice.
Hence it is glaringly obvious that this is a case of religious discrimination targeted at the practice of Shugden only. Only Shugden followers are discriminated against. The 2 reasons why Shugden practice is not allowed, are the reason that the practice will shorten the Dalai Lama's life, and the reason that Shugden practice obstructs the cause of freedom of Tibet. The first reason does not hold water because the Dalai Lama is Chenrezig and cannot be harmed by a spirit, unless he allows himself to be harmed. As for the second reason, concerning Tibet's freedom from Chinese rule, even with the ban on Shugden practice, Tibet is still not going to get its freedom or independence. The recent announcement by Barrack Obama says it all. The US recognizes Tibet as part of China. In other words, the US has stated unequivocally that it does not recognize Tibet's struggle for Independence.
Thus, we come back to the issue of Shugden practice as just being discriminated against for no solid reason. But with the discrimination comes the pain and the suffering of those discriminated against.
Why take away the pillar of Tibetan Buddhism, Guru Devotion, which ensures the survival of Tibetan Buddhism into the future, when spiritual leaders are no longer around, for the sake of 'political expedience'? Guru Devotion , the core of practice, came from the Buddha Himself. Ashvagosha wrote "the 50 Stanzas on Guru Devotion" in the 1st century BC and Tibetan Buddhism (arguably) began as late as the 7th Century in the reign of Bodhisattva King, Songtsen Gampo.