Kill processing may take long time. If it becomes terribly frustrating, try background kill processing using the following shell command:
emacs -batch -l gnus -f gnus-batch-kill NEWSGROUPS
where NEWSGROUPS argument is newsgroup names separated by either white spaces or a comma. `!' preceding a newsgroup name means negation, and `all' matches anything else. These interpretations are the same as the options line of the startup file (see section Startup File).