I think it was said that the Order has been around for about a century. It's possible/likely that Exorcists died at the hands of akuma, but I doubt too many of them got caught in that way (just the really inexperienced or stupid ones. Level Ones are pretty easy to take down, apparently). Finding Exorcists is apparently not an easy task, although it's what the Generals do. Of the Exorcists that we know entered the Order in the past few manga-years, three came on their own (Bookman, Lavi, Allen), one was the result of a regular mission (Miranda), and two (Krory and Chaoji) probably would have remained undiscovered, and Chaoji without Innocence, had the Exorcists not been sent to guard the Generals (technically, Cross was responsible for Krory, but he kinda abandoned the vampire-guy, so...).
Reinard said that the one akuma soul becomes responsible for both of those involved, I think. It's also possible, if unlikely, that the souls merge or something... Allen doesn't see the soul as looking exactly like the person who summoned it, and that could be responsible for the degrading of the soul at higher levels to make it look less like one being (the suffering, too; if both souls are suffering, it suffers more. =P But that's probably wrong).Now if I remember right, the soul is the power source of the Akuma (the more it suffers the more power the Akuma gets). With this in mind it may seem like a Purgitory type of thing (suffer x years for your sins as an Akuma, and be released) in which case the Earl possibly works for God. Yet what about the sins of the one that summoned the Akuma? Since it isn't their soul, and Allen can see the soul (note he always only sees one soul) suffering, the second soul is probably condemed. I don't think that this would be following the Christain beleifs at all (why give up half of the children, when you state that the end will come when all worship?). Also if we are going into metaphore here, the "apocolypse" the Earl is aiming for might just be that of the Akuma instead of the world.
The Apocalypse, for those who believe in the literal Second Coming/Rapture/whatever, is for humans on Earth. Not sure what you mean by "that of the akuma"; do you mean that only the akuma will be destroyed, or only the akuma will remain, or...?
(Another interesting note is that Road mentions something around the time of the Ark arc about the Noah being "sacrificial lambs". If the goal of the Earl/Noah really is to judge humanity, then it makes sense that the Noah aren't going to survive it, either. They're still human.)