The doctrine of disconnection may sound inhuman and atrocious, but it's also similar to what happens in other religions. Many Christian groups, like the Amish and Jehovah's Witnesses, practice some form of shunning whereby apostates and ex-members are ignored and denied access to family members who are still part of the religious group. It's not unusual for members who have doubts and questions to suppress these first steps towards freethinking and freedom because one price of liberty is to be closed off from all the community, friends, and family you may know.
This sort of behavior can be important to small and/or young religions where the loss of anyone threatens the group's long-term survival. In such cases, it's better to cut off contact with the doubter lest they use their emotional connections to get others to doubt as well. Because Scientology is a relatively recent religion, and thus has been small, it's hardly surprising that they would adopt the same harsh behavior as other small groups.
On the other hand, now that Scientology is also very wealthy and powerful, such behavior looks more like spite and nastiness than a desire for self-preservation. Some critics also contend that Scientology's disconnection policies go much further than the shunning practices of other religious groups. Scientologists are made so dependent upon the organization's social structures (one of the reasons it is called a cult by critics) that threatening to kick a person out means threatening to remove all social support systems from their life. It's no surprise, then, that members of Anonymous would protest the Church of Scientology in order to draw more attention to such policies.
The Church of Scientology denies that "disconnection" is an official policy and insists that individual Scientologists choose freely to disconnect all on their own. The denials aren't very believable, though, given the overwhelming evidence and testimony not only from former Scientologists, but even from Scientology documents. Denying their disconnection policy ultimately makes the situation worse because it makes them look more secretive than is necessary. As has often been pointed out, the cover-up can be worse than the original problem or crime.