all of those 'deities' are manifestations of Buddha. There are benefic and wrathful ones. The wrathful or malefics like Dorje Shugden are as Nun Jenchang said. They clear obstacles on the path to enlightenment. They teach us about our negative passions and shadows that hinder us and continue the suffering of ourselves and others.
I have not had any personal contact with Geshe Kelsang nor his group. I have read some of his books, and I did find them well-written. I do believe he does have compassion and wants to assist others along the Buddha's path.
I will say this. If you have any hesitations or feel 'disturbed' at all by anything that you are doing with that group, please leave. There is nothing in the Buddha's teachings that will, should, or have caused such feelings for those who choose to take up the challenge he put before us. I have been to numerous sanghas from a variety of traditions and done many empowerments and teachings for many decades now. I have never felt even once like any of the men and women who taught me were anything but honorable and honest. I always felt 'good' in their presence. I have never felt even once like any prayer, meditation, or practice did not sit well with me or was personally disturbing, and I have participated in several Highest Yoga Tantra empowerments that were certainly intense but never once disturbing.
Always trust yourself and how you feel when following any teaching, philosophy, spiritual path or religion. Always.
Good luck.