A line within the 8 verses, which is most apt for the Dorje Shugden ban and situation is this:
I will learn to cherish beings of bad nature
And those pressed by strong sins and sufferings
As if I had found a precious
Treasure very difficult to find.
This applies to both sides. People against Dorje Shugden practitioners should embrace them all the more. Seeing them as "bad" people, shouldn't Buddhists extend all the more kindness and cherish them all the more closely? We extend metta and compassion to animals and hungry ghosts, we pray to be able to benefit all sentient beings, but if someone holds a different religious belief, we slander and attack them? How is this congruent to any of the teachings of Dharma? To say that we are "attacking" Shugdenpas out of loyalty to Dalai Lama is to think in a very small way. Yes, the Dalai Lama has said not to practice Shugden, but he has also, as in these teachings, taught us what it means to practice kindness to all beings in the most practical manner. Why do we choose to follow one teaching and not the other?
This verse (actually, the whole prayer) also applies to Shugden practitioners - to not react to dalai lama and his followers (anti-shugdenpas) in the same way that they are being treated. Eye for an eye, tooth for a tooth never works, especially not when we are trying to practice. If people are acting in ways that are of a "bad nature" towards us (whichever side we're on), the rule of the game, I think, should always be to cherish them all the more closely. Find other methods to get our message across - such as to promote positive qualities of the practice, partake in education so people will be able to dispel wrong view and begin to understand things in a more positive way. And also to dedicate our merit to the people we perceive as being "wrong" so that they can get wisdom and a clarity to act in more kindly, beneficial ways.
I think above all, it is important to consider that the Dalai Lama has not just given teachings about how "bad" Dorje Shugden is. He has also given a tremendous wealth of other teachings on compassion, kindness, tolerance, patience, lojong, 6 paramitas. If we are true followers of the Dalai Lama and wish to be loyal to him, we would show the best example by practicing ALL of what he teaches. Hidden within that, I believe, is to practice tolerance and kindness to ALL, including Shugdenpas or to anyone who we might mistakenly perceive as being "against" the Dalai Lama.