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Well if it's Javascript then why not use Jquery to select the different links and add it once it's on the website? Or make an eventListener which checks for external loading and them for all Iframe elements check if the links contained are with the nofollow tag? Or you can try some delayed (asynchronous) loading of the script, this way google bot won't see when fetching it? (This said, I don't know if googlebot takes in consideration asynchronous loaded ads or not, try to fetch like google in google webmaster tools and compare the two versions..). Hope this helps.
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