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When doing things like git repack from the command line, a pack gets locked and can’t be removed, thus doubling the repo size. The culprit is most probably EGit holding the file open (which is bad in Windows). Exiting Eclipse is the only workaround I know. I’ve found this article, but there’s no such option for EGit. Any other idea?
The “Startup and Shutdown” option is the only way to disable a plugin as mentioned in your link (“Temporarily disable Eclipse plugin“) or in “How to disable plugins in eclipse 3.6 Helios ?“.
If you were building a plugin, you could then use a different target platform (as in this thread and in the comments of the article “[galileo] Manage Plug-ins in your Eclipse IDE“), but this isn’t the case here.