Content Keywords report within Google Webmaster Tools does not represent how Google understand the relevancy of your web site. The keywords shown in Webmaster Tools are based on the keywords we find when we crawl your pages. They are not representative of how we view your site's relevance in web-search, it is purely a count of words from crawling (so if you see some words there which are common on your pages but which you find irrelevant, I wouldn't worry about it).
If you remove those pages from your site, the next time we attempt to crawl and index them, we'll drop those keywords from our records -- and with that, over time, from Webmaster Tools as well.
Via Bonnie Burns, paulo oliveira