As someone who, once upon a time, identified (at least philosophically) as a Tibetan Buddhist, and still takes inspiration from Mahayana, I hope my opinion will be welcomed here.
I think the whole Shugden controversy is absolutely ridiculous.
One side is choosing the side of a very well known teacher and is condemning Dorje Shugden practice as evil. As something Adharmic. The other side is defending it to the bone and says that is it perfectly permitted within Gelug practice.
I, on the other hand, only see people who seem to miss the basic point of Buddhism. Metta and loving kindness; compassion for all sentient things; finding your own truth and not simply following something, because it is stated by a teacher or book. I don't see that when I see this particular controversy. All I see is blind sectarianism and fringe fundamentalism. From both sides.
Of course, nothing is black and white. The situation is certainly not as simple as I probably made it out to be. However, this is my observation and opinion. As far as I'm concerned, Dorje objectively has no real power and is only given power by those who either love or hate him. The same goes for the Hindu deities I revere. They, to me, have a personal power; because by revering them, they subjectively have meaning to me. The same goes for supporters and opponents of Dorje Shugden. Until people can separate objective logic with subjective emotion (which probably won't happen for many), then I don't really see this controversy ending anytime soon.