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Currently the History view shows binary resources in commits as well in the description area. We could reuse the File Content mapping of Team to determinate if we can show the files or not. The files should still be comparable as the compare editor can figure it out itself. As an example, see commit 7d64211cf2cb80492a9a6ee40752b7b77f78bb7a (Distinguish "Push" and "Commit" icons) in the History View.
With commits a8b29afd82795b3d98b42bf (JGit) and 7445a9123e5a7f4b85 (EGit) there is now the ouput "Binary files differ" similar to the one in gitk or in the diff on command line. I think that this bug can be closed. Please reopen if you are not satisfied with this solution.