Interesting question. I do not really know. Just to get the ball rolling:

You could use AppleScript to tell the Finder to eject the CD. Call this AppleScript from Perl using the "osascript" command line shell (or using Mac::Glue).

Or the 'disktool' command: disktool -e disk2. You need to know the name of the disk, however (disktool can also list the disks currently mounted).