Since there is already an option to check for mod updates, are there any plans to add an auto updater? Fine control over accepted release streams, or trusted mods could solve all issues users migth have with this feature.

Unfortunately, removing loaded jars is not possible currently on (at least) Windows without some sort of special Fabric hook which doesn't yet exist. I recommend launchers like the Modrinth App for this purpose, since they will be able to manage mods far better from outside of the game

FYI even on Windows what multiple popular mods do is they replace the jars when the game restarts, and use the JVM shutdown hook.