I believe you have already checked out your root Guru (Geshe) before you follow his teachings and all the practices that he gives you. Once we have checked out and choose a Guru, we should follow through all his instructions as he will know what’s best for us.
If you have doubts on Dorje Shugden, I suggest you checked out on this forum and dorjeshugden.com. For me, DS has been practiced by all the great masters (http://dorjeshugden.com/wp/?page_id=37
) such as HH Kyabje Pabongka Rinpoche, HH Kyabje Trijang Rinpoche, Kyabje Zong Rinpoche, Kyabje Domo Geshe Rinpoche, His Eminence Gangchen Rinpoche, etc and even the previous HHDL. Would these Masters wrong? Therefore, I choose to believe that HH Dalai Lama has a bigger picture for the ban.
DS is a protector practise that supports us in our spiritual journey by removing obstacles and creating more positive conditions for us to practise. Although as of now I may not be able to practise DS openly due to the ban, personally DS has helped me a lot to clear a lot of obstacles in my spiritual journey and I have more chances to practise Dharma and be connected with my Guru. I am sure he will help anyone who believes in him too. Therefore, I strongly urge you to just follow your Guru’s instruction and practice.