amavisd home is /var/amavis, and pid file is not overridden, so it is /var/amavis/amavisd.pid. However, the stop() function in the initscript codes it as /var/run/amavis/amavisd.pid, so the "/etc/init.d/amavisd stop" fails.
I was apparently working with the wrong copy of amavisd.rc6. The sed logic is now fixed in the ebuild. Thanks for the bug report; good find!