It could probably be improved (subject to the nuances of S3 which I'm not fully familiar with). One way to fix it would be to copy the concept of SQLite's WAL mode. Use an appended write operation on S3 (if it supports it) to append to an existing file that contains the transaction log. Then at certain intervals (say every few thousand transactions) one can finally flush that log to be stored in the main database file.

This would substantially reduce the number of times the database would need to be re-uploaded in full.