This is already how it operates.
Let me guess, running on Ubuntu with Upstart controlling the starting/stopping of sonnar (drone)? If so, the auto update mechanism doesn’t work, because the update process starts, which causes NzbDrone.exe to terminate, which in turn causes Upstart to restart it, which prevents the update process from updating any files, so it fails. Since upstart requires root/sudo to stop/start we can’t easily work around this issue, except for a custom update script that would have permissions to stop/start, not sure how feasible that is.