Why would the fact that the ventilation fans were on with the shafts open make a difference for the bad guys? It's not like a garden shed, big rig, or a projection booth are exactly the most airtight places either. Aha! While not airtight, the air inside is stagnant. The comet must have put a short-lived pathogen in the air in addition to whatever it was that steel stopped.
Why do they have guards posted when their installation on a now depopulated planet is so far out in the desert you need a helicopter to get there?
Probably a combination of keeping watch for uninfected survivors and creating a degree of "normalcy". Sort of like how Carl was doing homework on The Walking Dead. There wasn't really a point to it, but it gave him something to do.
Considering their own people were starting to "regress", the guards were probably intended to enforce internal security more than external. All they'd need is one degenerated lab tech to sneak out and trash their helicopters on the landing pads, and they'd be stranded.