Process was intentionally killed - now the process is still showing in "show processlist "
The process is undoing its changes after being killed (that is why killing write processes on a long running transaction can be dangerous- it can lead to a long undo process with blocking).

The rule of thumb is that InnoDB's UNDO can take multiple times the time it took to write. If it is unsustainable, you can stop the server when ther is no more write activity and restart it skipping pending UNDOs (so it doesn't start again). This is done with the start option:

innodb_force_recovery = 3


Not ideal as a normal start option, as it could make you lose data. Generating a backup before the unclean restart (or in general) is always a good idea, even if technically safe assuming no other writes or undos are ongoing.