Have you dropped Rank? Javascript, Links & nofollow

I was doing some seo for a site whilst listening to a pod cast on Google. I heard one of the presenters talking about how Google now is able to look at links within JavaScript more and more these days. After moving some links on this site I came across a link to the site that supplies the SSL Certificate for the site that in this case is Geotrust.

The site was built using Magento and after finding the file that supplied the code for the certificate I noticed the Grotrust logo and link both came from a JavaScript file on the Geotrusts site. Now in the old days i didn't have to worry about a link generated by JavaScript but these days it's probably going to be noticed by Google.

The link that comes from the Javascript file just shows the customer that the site SSL certificate is valid and has nothing to do with what we're trying to show Google. So I need to get that link to be a nofollow link but how can I do it without having access to the JavaScript file.

There's probably a way to write a bit of JavaScript to add nofollow to that link but then again I can't be sure Google will see it. I can't host the JavaScript file myself because GeoTrust might get funny about it or it might not work. So the only option left is to contact GeoTrust to try and get them to put up a nofollow version the script.

I can see a lot of sites loosing there rankings because of this fact. Definitely one to keep an eye on.