The answer to this question is actually given to us in the second chapter of this excellent novel, when Alice Cooksey is told of the contents of the telegram that Randy receives by Florence Wecheck and recognises the allusion that is made to the Book of Revelation in the Bible. She looks up the context of the verse:

And the kings of the earth, who have committed fornication and lived deliciously with her, shall bewail her, and lament for her, when they shall see the smoke of her burning.

Standing afar off for the fear of her torment, saying, Alas, alas, that great city Babylon, that mighty city! for in one hour is thy judgement come.

The implication is clear. The Book of Revelation talks about the end of the earth and the approaching judgement of the city of Babylon. Mark and Randy have used this phrase to refer to the approaching "judgement" or end of the USA. Alice Cooksey keeps abreast of world politics enough to identify the phrase "Alas, Babylon" for the warning signal that it is.