I'd proceed very carefully. Here's the problem - those same links from copies of your content that could potentially be causing you trouble with Penguin are also helping Google understand that you're the original source of that content. You could remove those links, still have Penguin in play and start getting outranked by the copies or even get hit by Panda on top of Penguin.
I would really want to see your entire link profile, because these kinds of links by themselves aren't that likely to cause a Penguin penalty. Obviously, your webmaster knows the site and I don't, buy my gut says that something else is going on here and that you've got other, more problematic links in play.
If these links are the problem, it may be better to disavow them in Google Webmaster Tools. That could help maintain the signal that these are copies but remove any negative aspects of the links themselves. Unfortunately, it's really situational and depends on the scope of the problem and your overall link profile.