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If deleting/modifying a file at one location results in deletion/modification of a file on the "backup", then it's not a backup.

Certainly. I remember learning early on that RAID != backup, and an easy conceptualization of Sync is RAID 1 at the file/folder level.

I'd recommend that someone using Sync for backup purposes take snapshots of they're syncing for backup purposes.

I can't think of any reason you would back up to AWS if you already have an offsite backup solution, unless you don't think your offsite backup location is reliable enough.

If use BitTorrent Sync, does that mean all your data is sitting unencrypted at the remote location? I guess that would be one reason.

The "encryption secret" was implemented in version 1.2 of BitTorrent Sync: http://www.bittorrent.com/sync/developers/api - but for now you'll need an API key to generate them.

Alternatively, you could roll your own solution on top of Sync by encrypting your files on your own and creating a Sync folder of the encrypted files.