Professor Thurman's Columbia University colleague, Modern Tibetan Studies program director Robert Barnett, confirmed the existence of an official prohibition of Shugden prayers by the Dalai Lama himself. This is a strong confirmation in face of denial by the Dalai Lama and Professor Thurman. Having written a book about "Love Your Enemies", Professor should just admit there is a ban and advise the Dalai Lama to lift the ban thus fulfilling his "Love Your Enemies" message.
In Buddhism, "the enemies" only exist within our mind and is the results of the delusions. It manifest from the ignorant mind that cherishes self (including the body, feeling, perceptions/beliefs etc) more than others. So, on the outer level, loving one's enemies is a way to reconcile our daily problems that results from hating the enemies. On a inner level, the enemies are the self cherishing mind. When that is conquered there will not be any enemies without.
Hence, Professor Thurman being the chair of Jey Tsongkhapa certainly understand this. It is just for him to practice what he preach. Otherwise, he should resign all positions from Columbia University.