License alert message for mysite.com, but not www.mysite.com
I'm worried that Craft might suspend the license because of the two different domains.


That will never happen, but from what you're describing you shouldn't be getting that alert.

Can you hit up support@buildwithcraft.com with some details about the domain name?

Regardless, you should probably be picking one of those (domain.com or www.domain.com) and forcing the other domain to redirect to it for SEO reasons.  Otherwise, the all-mighty Google will treat them as two different domains.