Well that's just plain stupid. You should only get flagged for a bounty by the faction you're doing harm to, and only if someone from that faction lives to tell about it.
You'd have to kill the Whiterun guards for this to happen, but then you'd have to kill everyone in Rorikstead too to maintain that hush hush no witnesses thing.
To much hassle. Just let them kill off the stormcloaks. You will get them all on your own and undisturbed when you see them wondering about on the roads or wilderness.
..and I'm really late on this thread