I hate it that we have to live with this type of fear.

- yeah, Sheldon: this and germs... :-)

But seriously, some of the sites of mine that went down the Google drain were clean, "link building" was not done, just attracted some real nice ones and yet the project died due to "penalties". I went out of answers to this somewhere in the middle of 2011 and focus on cool stuff, HTML5, content (I think some tools can be considered good content) and ultimately ranking solid on Bing. Google does whatever Google wants to do.

I wouldn't give it a second thought, especially if you're going to get traffic from the link. In fact, if it does send you traffic I'd go out and try to get a bunch more just like it! Get enough links that send you traffic and it won't matter what google thinks of them.

Leave that one alone. I'd focus on fixing/removing the low quality ones with that same anchor text.

One link from a quality, relevant website is not the problem. The hundreds of links with identical anchor text coming from blog spam, directory submission schemes and other short cuts are the problem.

I tend to focus more of my efforts on improving backlink profiles by adding quality links instead of focusing on deleting bad links. Even if you delete every single bad link (and somehow are lucky not to accidentally delete a good link) you still need to build legitimate links. So if you start working on legitimate links you may end up getting enough good links that it naturally defuses the bad link issues.