You can look at most groups and find beliefs that are damaging in one way or another. The issue isn't so much whether they believe things that undermine a person's autonomy but rather how those beliefs are implemented.
Most religions don't use fear to control and manipulate people. If a person wants to leave and join another group it usually doesn't cause much anguish. If they don't accept and follow every one of the beliefs it usually doesn't bring ostracism on them.
The concern boils down to whether the beliefs and practices are strictly enforced leaving a person who decides to believe something different no graceful way out.
Some strict Orthodox religions will literally tear their cloths and denounce a child who leaves the group. Just recently here in Ontario it is suspected that a brother (not a JW) killed his sister because she was seeing a man that was unacceptable to the family and therefore brought shame on them.
Religions that have a strictly enforced us versus them belief system are far more likely to be damaging to members who don't follow the beliefs than those who allow personal freedom. They may have a rule (like excommunication in the Catholic Church) but it is so rarely used no one would bat an eye if they found out someone was excommunicated