“If the leader of a cult is indicted, should all of their branches be shut down?”
No, that’s another example of over-simplified knee-jerk over-reaction.
The organizations of people who do horrible crimes should be investigated appropriately, and appropriate action should be taken.
Where I do think there should be changes, is in the case where an organization itself is found to be causing problems. In those cases, when an organization is systematically acting in ways that lead to damage to people and/or the commons and/or the environment and/or the general good, then I think it needs to become common practice to investigate and analyze such things and then re-organize and/or abolish those organizations and the people responsible for them.
Mainly I think that would apply to things like corporations that have a pattern of, say, causing ecological disasters, or interfering with democratic government. The corporations should have their charters and policies re-written so that they will stop or greatly reduce their problematic behavior, and/or be abolished and the bad actors prosecuted and barred from further such activities and from lobbying government, etc. No more fines that can be written off as expenses while the company keeps on doing damage.