Yes, I am paranoid of S3. Not only could a once in a lifetime event happen, an attacker could get in and delete all my data. Data could be accidentally deleted. Corrupted data could be written...
1. Use tarsnap so there's an encryption and a management layer.
2. Use a second service so there's redundancy and no SPoF.
3. Keep cryptographic signatures (not hashes) of each backup job in something like a WORM blockchain KVS.
You guys should really have versioning enabled. Now if someone deleted your data and all the versions, that could be possible, but that would take real effort and would like be malicious.