You’re not the only one, I kinda hate mup, so I run my own deployments using nginx and
meteor build. I’m pretty sure Meteor methods are cleaned up gracefully unless you hard kill the node process. Same goes for database writes, at least on MongoDB. Nginx has a graceful shutdown protocol as well, shutting down connections that first don’t have clients and then waits at least some time before killing active connections.
Depending on how fast your server(s) is/are this is a pretty marginal concern, especially if you’re using a job handler/watchdog like Upstart. Process termination protocols clean things up relatively nicely/quickly, and unless you have some long running methods, your users should have a decent experience. The only potential problem there is if you do have a lengthy method execution, restarting the app will cause the client to automatically re-run the method on re-connection (in most cases), which depending on what the method is doing can cause you to commit duplicate DB operations and stuff. There are some ways to mitigate that potential problem though, like making your methods idempotent, having a responsible data model, etc. I believe you can read up on it in the guide.
My best advice would be to test those edge cases and not worry so much about anything else