Does google knock you down for having a wordpress post that is in your archives and then in multiple categories? Just something i wonder with my site and me not getting a good PR.
I don't think it's such a big problem. You can use .htaccess file to resolve this if it's such an issue. Personally I can't see any difference.
Not too bad though. They're decent at detecting such things. Either way, the plugin is a good idea. For some reason didn't work on my blog, but if you need to just open the template up and no-follow all category/tag links, then set it so if it's a category/tag page, it has the NOINDEX tag.