The MW logo is PD content and Anthere and I explicitly designated it as such. I'm not even going to get into any discussion about whether we could retroactively "un-PD" it, as I find such attempts to put content that has been explicitly released to the public under a proprietary license unethical.
Is it valuable for the MW logo to be copyrighted by the WMF? Maybe it is, maybe it isn't. I'm skeptical. I've seen dozens of wikis which have "remixed" the MW logo to make their own (put something else between the double square brackets etc.). I think that's pretty cool and has not created any confusion as far as I know, since MediaWiki is primarily a product rather than a community website of its own.
I suggest distinguishing strongly between the brand name MediaWiki and the picture used to represent it. One can be protected while the other is not.