I recently started using Eclipse Kepler with EGit plugin and these branches are not what I am used to. Is there a way to permanently stop these branches from being created? I tried removing them manually, but it does not work and I don't want to have them the next time I do fetch or rebase.
As I understand from the comments on your question, you only want these refs not to be shown in History view.
You may try to uncheck Additional Refs from Preferences > Team > Git > History. This should do the job.