This thread: How to disable EGit temporarily? discusses how to disable EGit in Eclipse, but when I go to "Startup and Shutdown", there is no option to disable EGit.
How can I control what plug-ins are loaded in Eclipse-CDT?
To uninstall plug-ins or software from Eclipse:
I think in the latest release of Eclipse, you will NOT find eGit in this list. Instead you will find it under the features/plugins list. SO, it is not easy to remove. I would suspect you can still goto the Eclipse install directory and cherry pick it out but whats the point? Just follow bobestm advice and disconnect the project from git and CDT should not bother you about it (mine does not...)
You will not find eGit in the Startup/Shutdown preference anymore. I think what has happened is a much tighter integration of git into the IDE (and not with the CDT). This is a good thing, but I am not sure why you need it disabled.