I don't think CTA can do much, especially when it comes to persecution, how and with what authority can they exercise such power?
In my personal opinion, CTA is merely parroting His Holiness' reasons to ban Shugden practice. If they really want to head towards the direction of democracy, why not have a meeting with the monasteries and high lamas and vote whether or not the ban is necessary or even make sense? Perhaps debate it out?
By the way, Shugden practitioners do not cause harm (ok, there were some loud protests around the world by WSS), whereas groups and organisations out there that perhaps are misleading the public or their lineage appears to be a bit suspicious, I don't think CTA spend time to find out, nor it is under their jurisdiction to do anything about it.
Tibetan Buddhism doesn't belong to CTA, however they want to think. It is nevertheless their best export to the world and His Holiness the Dalai Lama is the best spokesperson, but it doesn't have to remain so.
Also, I do agree that this group is quite unorthodox. Some info about this group from their website:
http://www.jingangdhyanaincnet.org/Holy Tantra Jin Gang Dhyana Buddhism is Chinese Han transmission of Tantrayana Buddhism (previously called TangTantra).
It claimed that their tradition was a merge of three transmission from the ancestral masters of
Great Holy Jewel Nagna Hutuktu (Tibetan transmission)
Great Holy Jewel Dilouhua Hutuktu (Mongolian transmission)
Great Holy Jewel Jing Wu Great Dharma Lord (Han transmission)
And that the Heir of modern times (of course!) is: Holy Zhi Ji Vimalakirti Ahdharma Buddha The Most Venerable Patriarch Master WANG
It was said that the three transmissions merging to one in the twenties of the twentieth century took place at Ling Jiu Sheng Mi Tian, Peak Fei Lai, Hang Zhou, China.
After extermination of Buddhism by Wu Zong Emperor of Tang Dynasty (841-846), Chinese Han transmission Tantrayana completely concealed underground, relinquished temples to mingle with the common people, abandoned Sangha jewel form, giving up oneself for Dharma, sacrificing oneself to deliver sentient beings, concealed without revealing identity, conveniently followed conditions, established outdoor mandala which are called Sheng Mi Tian. Ling Jiu Sheng Mi Tian in Hang Zhou is one of the hundreds Sheng Mi Tian in China.