CDN for main blog of a multisite - impossible?

How do you configure CDN on the main blog of a multisite? I'm trying to use Amazon Cloudfront on

I can’t create a CNAME record for Cloudfront because you can’t create a CNAME on a root domain. That’s against the DNS protocols.

So I decided to let Amazon Route 53 manage my DNS. But it said:

Amazon Route 53 automatically creates a name server (NS) resource record set that has the same name as your hosted zone. It lists the four name servers that are the authoritative name servers for your hosted zone. Do not add, change, or delete name servers in this resource record set.

But I absolutely need my own name servers. They're authoritative for my clients' domains and are needed to map my clients’ domains to their websites on my server.

Am I missing anything, or is it impossible to run CDN on the main blog of a subdomain multisite?