It'd be hard to maintain a necessary amount of order in a wolrd like that. That is why they need to be so strict. I would be quick to lable them as bad guys. Instead of thinking about an eventual good apple among them, I'd think of them being kinda good, but having a few bad apples. The problem is that one bad apple can cause a lot of damage in a totalitarian regime.
I don't doubt that the military has executed large amounts of people simply because there aren't enough rations to go around and, as Joel said, "dead people don't get infected" and I bet there are population control laws as well, I'd imagine reproducing and adding another mouth to feed isn't too smiled upon.
However I kinda doubt they'd be trying to kill off our species simply because of apathy. The quarantine zones are quarantined as a way of preserving the last of us. So are the extremely strict protocols enforced. If they didn't care they'd just open the doors and let everyone fend for themselves.