Deregistration of a religious association – which would be a first in Czechia – does not mean a ban on practicing the religion, but the loss of additional rights given to officially recognised churches, including the legal status and possession of a bank account, the ability to perform marriages, or to teach in its own theological schools.
This is the worst possible fate for the organization. The primary restriction is financial. They can continue to meet, pray, and preach. But raising funds won't be as easy. And it's not the same kind of persecution as being banned. They are being asked to stop certain policies, which will make people more aware of those practices.
More governments need to do this. You can practice your religion, but it's not as easy to raise money, and your flaws will be put on blast.