I just saw this in the theatre and you bring up some very good points!
The gov't when they are interviewing Jude Law's character are telling him what they are going to accuse him of, but it's questionable whether it is the truth or not. He nods as though he knew that they would frame him in that way. Then the movie ends.

The movie shows us:

-Multiple shots of people taking the vaccine nasally, at which point they put on a bracelet to show that they are "safe"

-Security lockdown and checkpoints at state lines preventing people from traveling

-Riots and looting of stores and homes

-Mass graves for the dead

And you are right, the message is definitely that the vaccine is the only sane and safe way to stay alive, whereas natural therapies are quackery and fraudulent. This movie is blatant propaganda. They even had Sanjay Gupta (the Doctor on CNN) play himself.