For a more recent discussion about a similar topic check this question out.
What\'s the best way to validate whether a particular user has ownership of a website?
You could confirm it in a manner similar to what google analytics does by having them place some javascript/code on their site that you could use to confirm. Alternatively you could have them create a DNS record that you could check for - both of those would show actual ownership of the site rather than just being part of the domain.