To remove a service from chksrvd(cPanel’s monitoring daemon), you must edit the appropriate file in /etc/chkserv.d/.  For example, to remove tomcat from monitoring, you will need to edit /etc/chkserv.d/chkservd.conf, and change the 1 to a 0 next to tomcat.  The file will look similar to this:

root@cpdemo [/etc/chkserv.d]# cat chkservd.conf
clamd:1
cpsrvd:1
exim:1
eximstats:1
ftpd:0
httpd:1
imap:0
mysql:1
pop:1
spamd:0
syslogd:1
named:1
tomcat:1
root@cpdemo [/etc/chkserv.d]#

Merely change the the number, and then restart chksrvd with the init script in /etc/init.d.