As far as I know, there is no such thing as rel="follow" or rel="dofollow" , so adding to links will not work. He always suggested that links should be followed, unless otherwise indicated, and not vice versa.
EDIT : This post from Matt Cutts confirms that "nofollow" always takes precedence.
Using robots.txt will not work, because it only indicates which pages should be indexed or not. Nofollow, on the other hand, instructs to either ignore the link (if it is attached to the link) or all links on the page (if they are used in a meta tag similar to this question). Nofollowed pages can and will be indexed.
Unfortunately, the only route available to you is to fix a broken system that first adds meta nofollow.
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