I have thought about this before, long and hard. Why does the Dalai Lama treat Dorje Shugden practitioners with such wrath and have brought upon so much difficulty for the practitioners when they have done nothing wrong but hold on to the Dharma practice that has been given to them by their Gurus? And for adhering to their Gurus, they get ostracized, ridiculed, being kicked out of monasteries and things are being made difficult for them. Mind you, this does not just affect the Tibetans already, but it also affects many Dharma practitioners around the world who think that Buddhism is all about adhering to the Dalai Lama's advice even if it means that they dont know the real story or what is going on.
I am thinking, maybe, perhaps, HHDL is doing all this to make the practitioners stronger so that they can spread Dorje Shugden far and wide. The mental strength that can be accrued by going through the ban will definitely help to accelerate spiritual practice. If the Dorje Shugden practitioners can do their Dharma practice under such harsh conditions, where everyone else is against them but yet they still hold on steadfast to their Guru's instructions, even if it means that they have to suffer a lot of accusations and discriminations, it will greatly strengthen their resolve for the Dharma and it will cause these practitioners to attain results faster than those who dont. Proof? Look at how many illustrious Dorje Shugden lamas there are, including those who have "given up" publicly, compared to those Gelug lamas who were against Dorje Shugden from the start....
Another reason I can think of is that the Dalai Lama has noticed that there are too many insincere practitioners around and he would want to filter them off. From the ban, it is very easy to see that the sincere ones are the ones who adhere to their Gurus, while the insincere ones who just want to look good and have an easy life adhere to the Dalai Lama's command and even going to the point of denouncing their own teachers and Dharma brothers and sisters just to be in the correct side of the political intrigue because the latter are the ones that are not famous. FPMT's growth has stagnated ever since the ban. It was spreading and growing like wild mushrooms during Lama Yeshe's time (where Dorje Shugden was one of the core practices) but as soon as the students took over and decided to be rid of Dorje Shugden, growth of the centers stopped completely. The same can be observed in Ganden, Sera and Drepung, while Shar Ganden and Serpom is growing exponentially.
these are the conclusion of my thoughts about why the Dalai Lama implemented the ban.