Exactly, defederation is just a tool and it’s up to the owners to use it when appropriate and in line with their goals for the instance.

For example when brigading happened on Reddit some subreddits had to go private to defend themselves, with Lemmy the owners can defederate from the offending instance instead but still keep access open for everyone else. Another aspect is the legal side, as someone else also mentioned the content OP talks about is illegal in many countries and due to the way the Fediverse works owners of the federated instances will end up linking and hosting that illegal content on their own servers as well, unless they defederate.