After reviewing my content keywords in Webmaster Tools, it seems that Google is identifying the text in non-relevant links as keywords. Is it acceptable practice to implement
rel="nofollow" within the script of these links?
Like I said (dramatically and poorly) in my comments, it is not an acceptable practice. nofollow is designed for webmasters to disavow links on their own website that they do not have editorial control over. The best example of this are blogs with links to the websites of commentors. This was a common source of spam and this allows blogs to allow the users to include those links but they have no SEO value. That is not the case here.
Using nofollow to attempt to manipulate how Google crawls and views your site is a bad plan. Just because Google sees those keywords on your site doesn't mean it doesn't see the other keywords you are trying to rank well for. It sees all of them. And those internal links are helpful for Google to find and index your pages so they're good to have.
If you can't change the anchor text to better keywords then leave everything alone.
Keep in mind that if Googlebot sees a nofollow on a link on a page, then it treats every link on the page with that same URL as nofollow.
Consider this senario: You have two links on the page to
myotherpage.html. The first link has the anchor text "Click Here" because it is prominent to users and usability testing shows that having action words increases the click through rate. The second link has the anchor text "my target keywords". You'd like Googlebot to ignore "click here" so you apply a nofollow to the first link. The problem is that even when the second link is plain, Googlebot treats both links as nofollow. You are not passing any pagerank at all to
Google never intended nofollow to be used for directing Googlebot within your site. People have tried to use it to sculpt pagerank or to try to manipulate the keywords that Googlebot sees. Neither approach works well. There are just two many pitfalls that are easy to get into.