NVD3, a d3.js reusable chart library, was taken down by Novus several months ago. At first they asked all the GitHub forks to close down. Eventually, after an outcry on the d3-js Google Group, Hacker News, and other forums, Novus relented and re-released the library with this statement:
Yes, this is EXACTLY the response that we are looking for.
Not that the company is necessarily in the wrong to ask that the open source code be taken down, but that the community should persuade that company that it is in their interest to keep the code available. (For reputational reasons AS WELL AS all the other benefits of supporting open source.)
http://nvd3.org/statement.html