No, there is no truth in this. The New Kadampa Tradition (NKT) has no wish to harm the Dalai Lama.
During the protests against the Dalai Lama’s ban against the practice of Dorje Shugden, Dorje Shugden practitioners like those in the NKT asked the Dalai Lama to stop hurting people — and himself — by suppressing religious freedom. They never expressed a single malicious intent toward him.
In general, harming or wishing to harm other living beings goes against the teachings of Buddha and every precept in the Kadampa tradition. The Dalai Lama is not the NKT’s enemy. NKT practitioners are taught that their only enemies are the delusions in their minds, such as ignorance, aversion, and attachment; living beings are always the objects of love and compassion. Training in compassion is indispensable for Kadampa Buddhists because it is the main path to temporary and ultimate happiness, and it would be contradictory to be training in compassion but secretly wishing for someone to be harmed.