It has been a long time strategy of ours to remove ANY site that is linking to us sitewide. Email the webmaster and ask him to make your link a homepage only link. Sitewides are discounted at best and penalized at worst so I would recommend removing all of them when you come across them.
They usually come in form of a blogroll link which has been a bad method of link building for many years, and your sitewide link is lumped in with other sites in the blogroll who all have sitewides as well, so their chances of getting penalized are greater too. Then you will be listed sitewide with a penalized domain which is linked sitewide. So now you share a more similar link profile having thousands of links on the same page with a penalizes site or sites. AND you have thousands of links with the same anchor text. It just bad all around.