I think Samdhong Rinpoche is a great being. He has great Guru Devotion and was and still is a good politician. Sometimes we tend to look at things on the surface. When he was the PM, he implemented the policies of the HHDL basically. That being the case he was "anti-Shugden" simply because HHDL was anti-Shugden. It we look deeper, monks like him practices Guru Devotion, first and foremost and that means everything that the Guru ask him to practice or do. Sometimes the Guru instructions is contradictory, but he took it in stride.
Beyond, anything I think, he showed to the world that while HHDL policies are supposed to be non-sectarian; by banning the the Protector and the HHDL is sectarian. That is the irony he showed.
Going forward, Samdhong Rinpoche is probably one of the best person to mitigate for the ban to be lifted as he is friendly with HHDL/CTA and Trijang Rinpoche.