Hi,
I'm not sure why the plugin was writing anything, since all it needs to do is read the files on the server and write them to S3.
S3 is not capable of constructing a zip archive at its end (nor is any other cloud storage solution) - therefore, backup plugins have to create the zip archive on the local webserver, then upload it to the cloud storage, and then delete the local copy.
If you need a backup plugin that does not create zip or tar archives, but instead sends the files directly into a full directory tree at the remote storage side, then the only mainstream one I am aware of that does this is: http://wordpress.org/plugins/wordpress-backup-to-dropbox/
there should probably be a limit to how many times the plugin keeps trying.
There is - after 10 attempts to run a backup, no further attempts will be made.
Best wishes,
David