The Crossed germ is ancient and predates human history.The only basis I have for this is the covers, but on some of them it appears that ancient civilizations have succumb to the virus before(archaeologists finding cave drawings of the Crossed, the Mayans showing up Crossed, etc.) Perhaps the virus is far older than it appears, and is something that has been with humanity for as long as humanity's existed, occasionally causing outbreaks that result in mass deaths. And in relation to that....
The Crossed germ caused many of the historical massacres and disappearances that cannot be explained.From Roanoke Colony to the Mayans to any other event one can think of. Maybe they were caused by the Crossed germ "activating" somehow and killing off a large percentage of the human population.
The Crossed outbreak is God "correcting" Humanity back to its intended stateAccording to the Bible, God originally intended Humanity to have no conception of right or wrong and thus be completely innocent - the knowledge of good and evil was a corruption of Humanity that He did not want. The Crossed virus is His final solution - returning everyone to their natural, much more animal state, with only one extra impulse - to propagate the virus throughout the entire species as forcefully as possible. In a universe with God, everybody being Crossed is actually not bad - they all seem happy enough, and the constant death really doesn't matter since, everyone being innocent again, they'll all end up with God anyway. The X-faced nun from Wish You Were Here is actually his last Messiah, since she actually led a truly good life of total purity, she's worthy of Heaven without needing innocence, so she's the perfect candidate to infect with a variation of the virus that grants heightened intellect and awareness so as to lead the Crossed more effectively to claim the last survivors who have formed strong holdouts that leave them possibly safe from regular, chaotically organised and unstrategic Crossed groups.
Aoileann isn't Crossed at allWish You Were Here has already introduced the idea that some people might be immune to infection. If Aoileann is one of these, it would explain why she doesn't have the rash despite getting dangerously intimate with the Crossed. It also means that her experiences with Shaky and the Gamekeeper must have driven her to the kind of madness which can terrify even the Crossed. This also explains her companion in the home-made biohazard gear; whoever it is, it's Aoileann's ally, and it suits her for them to remain uninfected. Otherwise the regular Crossed would just tear them apart.