I trusted that the "Check default remotes for updates every X minutes" would delete remote branches automatically. However, much to my surprise and my team, people were pushing up old deleted branches because they trusted the automatic refresh was pruning them locally.

I suggest that you add a checkbox in the Preferences to add the PRUNE option to the fetch (git fetch -p) so users can truly appreciate the automatic refresh and not have to worry about having to fetch -p manually.