When hackers bring down a website, they're not really damaging it; they're just blocking your access to it. Here's how distributed denial-of-service attacks work, and what website operators can do to avoid being knocked offline.
I think you missed a major part in your article about how to survive and mitigate a DDoS attack...
Services like Cloudflare and Incapsula are a security layer between the client and server and are designed to mitigate DDoS attacks. They do this by spreading the requests across their huge network and by blocking malicious traffic. They're also more like traditional CDN's (Content Delivery Networks), which means they generally speed up the site performance too.
It's also worth noting that DDoS via BotNets (which you refer to as "zombie" computers) is bought in time slots, so a DDoS attack is normally only temporary. From a cost point of view, it would make more sense for someone to use CloudFlare than to invest in their own load-balancing servers (which would probably be overloaded anyway).