Instead of copying Eclipse.app around, create an automator that runs the shell script above.
Run automator, create Application.
choose Utilities->Run shell script, and add in the above script (need full path to eclipse)
Then you can drag this to your Dock as a normal app.
Repeat for other workspaces.
You can even simply change the icon - https://discussions.apple.com/message/699288?messageID=699288