I can actually see that working quite well. Something with Tony telling J.A.R.V.I.S. to put up firewalls or something and J.A.R.V.I.S. replying that Ultron is getting through or something and that options are extremely limited, there needs to be a reactionary firewall, etc. etc. Then Tony asks J.A.R.V.I.S. for an update and there's just silence. An interesting way to kill of a character without actually killing off one of the humans.