IMHO:
1/ Drop hints. "Sir Cedar von Oaklarch passed through here on his way to slay XXX... he hasn't returned, but his squire was found. Poor lad's in the jail house now, he wouldn't tell us anything and he keeps screaming at night..."
2/ Make it hard to find the BBEG. Why would such a being be accessible to low-level PCs?
3/ Drop the hammer. If they persevere to find the BBEG, fine, have him kill them as quickly and efficently as possible, and then laugh! Laugh at their misery! Bwa-ha-ha-ha-ha!!!
-- N