There would seem to be good points on both sides, so until it gets tested in court, I don't think we'll really have an answer. The issue is also discussed, though without a clear conclusion, in Wikipedia's article on the GPL [1].
Personally, I don't really like the FSF position (at least not to the extreme they push it). Everyone agrees that copying code is generally derivative but counting nearly all form of code interaction as also derivative feels unnatural. In this circumstance -- and irrespective of what the law actually says -- it would seem more natural if software were treated more like a physical object subject to first sale doctrine and similar principles. For example, it seems more natural (to me at least) to say that an end-user should have arbitrary authority to modify and combine legally obtained software, but not be allowed to distribute copies of the modified software. To give an analogy, car companies do not have the authority to restrict after-market modifications to the chassis of a car, and there is a booming industry of people providing after-market mods. So why should software copyright holders get to control the skins used in conjunction with their software?
That said, a lot of the copyleft movement has operated on the assumption that copyright holders have nearly arbitrary freedom to impose restrictions on the users of their works. And maybe that is true. For the most part it hasn't been directly tested. I don't know whether the FSF is right about the reach of the GPL with respect to APIs and linked code, but personally, it feels like just another piece of evidence that copyright law needs to be updated to deal with the realities of the digital age.
If there is a decision to be made (and I'm not sure there is), I would personally argue that we should take steps to make sure that authors are informed about the FSF position on the GPL, but not try to enforce it ourselves (except possibly for the extensions and skins actually deployed by Wikimedia). I don't see much benefit for Wikimedia in taking a hard line with third-party software contributors over the licensing of their extensions.
[1] http://en.wikipedia.org/wiki/GPL
-Robert Rohde