I rather like this idea, as it meshes rather nicely with the "mechanical" aspect of Azerothian lore - Algalon as an antivirus program, Re-Origination as reformatting, and the Emerald Dream as a post-install backup image.

Some giant Titan-created machine forms the "core" of Azeroth, which in turn forms the rest of the planet around itself. The "Matrix" that keeps being referred to could be something like the core programming of this machine - the "blueprint" of the planet, as it were.

The Old Gods corrupt and infiltrate the core programming, inserting *themselves* into Azeroth's code - ensuring that were they to ever "die", Azeroth would just re-make them. (Malware infesting the boot sector?)

From there, they initiate the "Curse of Flesh", subtly re-writing the blueprints/patterns for other Azerothian life, to make them easier to corrupt. (Reverse security patching?)

Mortals come along and kill parts of the Old Gods (functioning sort of like a preliminary malware scan/remove process), and manage to "clean" the infection from some parts (Watchers in Ulduar), but the greater infection "lives" on.