I believe you are talking about quarantine here?
Here in North Carolina, they don't plan to shoot you, according to their updated Pandemic Plan. The penalty for breaking quarantine is merely to arrest you without bail (maybe quarantining you in the nearest guarded school gym with 1,000 of your newly acquired, closest, quarantine-breaking friends?) followed by up to two years in prison - if you survive the gym. Hopefully, the disease won't break out there!
But shoot you? No!
"But shoot you? No!"
Way back in the early 80's I had a job reviewing and drafting military and natural disaster plans. At that time the classified plans did indeed cover mandatory quaranteens and shooting those out and about.
Under a biologic attack, the assumption was that the area would be quatanteened and anyone trying to leave is disuaded forcefully....not rounded up and not quaranteened, stopped.