The military was right; the protagonists should have been shot
Perhaps some my find this interpretation controversial, but it's clear that the Tammy and Andy were at fault for all of this.
Though understandable that they would want to return to see their home, the discovery of their mother after bending the military containment rules set the plot on the path to hell.
General Stone was correct to have put on a code red, even killing potentially innocent civilians given the threat and what was known about the virus: It's immmediate and deadly spread, and the constant threat of it crossing the English Channel. There is no doubt anyhow that the procedural policy was decided by higher echelons. He was only there to judge when/if it should be put into place.
Doyle was wrong to have asked his comrade to bring them across the Channel as the film clearly implies that this is what brought the French outbreak.
The lesson of the movie? Perhaps that individual wants and moral calls can be an anathematic to the collective result.
The other though provoking side of the movies is exactly this question of responsibility, and the viewer wrestles with it from the beginning. What would you have done in Don's shoes? In the soldiers' shoes? In those of Tammy and Andy? In those of the pilot that makes the fateful flight across the channel?
Excellent movie. 9/10