We did! Our infrastructure has some unique constraints around filesystem persistence. We use btrfs and regularly take snapshots of the repl's filesystem while someone is editing the repl. However, we don't take snapshots when a repl is only acting as a web server without anyone editing it, meaning that we would need a solution that lives outside of the repl's filesystem.
Keeping each database outside of the filesystem also gives us the flexibility to let people access the same database across multiple repls in the future.
I have lots of love for SQLite; early prototypes of Database were backed by it!