For the sake of clarity, the first news I saw about the EFF stopping accepting of Bitcoins was two weeks ago:
EFF no longer accepts donations in Bitcoins (bitcoinmoney.com) | HN link
The EFF blog post is I think an announcement insofar as to address the kind of news above that was floating around but mostly an explanation.
The EFF has stopped accepting Bitcoins primarily out of concern with the possible legal issues. I presume that the EFF has a better understanding of any possible legal risks than organizations like the SIAI. It seems that the SIAI should probably at least for now put a hold on accepting bitcoin donations until these issues are resolved.