Like seen in The Hot Zone book and the Outbreak movie, there are possible chances of a dangerously lethal disease hitting a populated area, a terrifying worst case scenario involves the imminent deaths of many, along with a high chance of the disease spreading from area to area at an unsuspecting rate. The government must do their job to defend their country from such threats, but how far should they go if such a lethal disease is present??
If a virus similar to the "Motaba" in Outbreak hits a town, quarantine is top priority. Nothing with the possibility of carrying the dangerous disease comes out, and yes, the usage of military is recommended. Sure, it may seem degrading for the civilians to see how dangerous their town has become, but it's probably the only way to keep order in a chaotic state. In the town itself, separating the people with a normal status from people showing symptoms of the disease in them cuts the chance of the disease infesting more people.