There are a number of methods for removing emails from exim queue. The following one is a generic method , but it is slow ,
#exim -bpru | awk {‘print $3’} | xargs exim -Mrm
But using a generic find command is easy , because it will remove the spam email files on-the-way .You can use the following find command to remove it from a cpanel exim server.
# find /var/spool/exim/input/ -type f -exec rm -vf {} \;