Rather than be concerned about the PR part of it, just correct it. If you don't want the IP address to deliver the site content pages you can either set up a default virtual host container for the IP with just an index page or you might even consider redirecting that IP to your primary domain name.
You should install code to 301-redirect all non-canonical requests to the canonical domain. For example:
Redirect 188.8.131.52 to www.example.com/ example.com to www.example.com/ <anything but www>.example.com to www.example.com/ <IP or domain>. to www.example.com/ <IP or domain>:80 to www.example.com/ <IP or domain>.:80 to www.example.com/ <IP or domain>/index.php to www.example.com/
If you do not use any other subdomains except for "www", then this can be done with just a few lines of code using Apache mod_rewrite or ISAPI rewrite on IIS. Alternately, if you generate your pages using scripts, then you could include PHP or .asp code to do these redirects.