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.
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.