Hi GP,
the installation of dolphin, or the setup of the sitemaker must have made some reference to the ibay for the script to be calling it. (think how else the ibay would be known to dolphin...) you mention that the complete installation is in /opt/dolphin, I would assume that all scripts in dolphin have either a configuration file that references a base directory or are relative to where they are running from. are you sure you don't have a config file referencing the ibay? the ibay should be playing no part in the installation at all. correct?
You can check the settings of sitemaker from the console, the folder below will hold the sitemaker details you setup when you ran the sitemaker script:
/etc/e-smith/templates-custom/etc/httpd/conf/httpd.conf
Dolphin config files should be in the /opt/dolphin folder.