What's the Fly.io issue here? Aren't the issues you're describing in Rails not Fly.io?
I run several Go apps in production on Fly.io[0, 1, 2] and I've never had an issue with the Fly.io + SQLite part of it.
SQLite + Litestream makes things slightly more complicated, but again, I've never had issues with Fly.io specifically making that harder. I use a custom launch script in my Dockerfile that starts litestream with the -exec flag to start my app as a child process.[3]
[0] https://github.com/mtlynch/logpaste
[1] https://github.com/mtlynch/picoshare
[2] https://github.com/mtlynch/screenjournal
[3] https://github.com/mtlynch/logpaste/blob/0.3.1/docker-entryp...