OK, so having the same problem with Safari and doing a google search led me to this Apple discussions page. Basically following these steps (via @evenhuis) you can re-map the quit shortcut to any other menu function:
- Go to System Preference > Keyboard.
- Choose Keyboard Shortcuts
- Click Application Shortcuts
- Press the + button
- Under Application choose Eclipse
- For Menu Title input "Show All". (You could use some other innocuous menu option here)
- For Short Cut use ⌘Q