A federation is just a group of entities that has agreed to work together.
De-federating means that you don't want an entity in the group so you refuse to work with them.
For the threads situation. Say all of the nerdy kid's in high school decided to make a club (current fediverse) and one of the popular kids (meta) wants to join, but the existing nerdy kids in the club feel that the popular kid is really only joining to take over and ruin their club. Many of the nerdy kids will ignore the popular kid to try to freeze him out of the group (defederate).
Some existing members try to block, some will accept, and some will wait and see what happens. In all cases the popular kid has already disrupted and created divisions in the original club members.