I had the same problem. Here are the steps to resolving this.
- Go to the Organizer (under window menu option)
- Go to Repositories
- Look at the bottom left corner for the minus button
- Select the project to be removed from GIT
- Press the minus icon
- It should be removed
This works, even though the class files still have the symbol next to them. Clicking them then clicking another file gets rid of the icon.
Hope this works.