From a legal standpoint, the EFF is not legally required to gain your approval before spending their money, yet you seem to feel that it is appropriate to air your complaints (FWIW, I agree with your right to air them, even if I find your complaint contradictory).
Github have made commitments to protect free expression (for the hard of thinking, freedom of expression includes free speech) so it seems quite reasonable to take them to task when they seemingly break this commitment. It's a shame that so many seem to have forgotten AACS (and, more recently, youtube-dl) and what it meant for private sites standing up for individuals in the face of underhanded legal pressure.
I get the feeling that much of the support for Github comes from the more myopic cryptocurrency opponents who are happier to see a little suppression now at the possible expense of their freedoms later. Again, while these aren't legally guaranteed freedoms, how we respond to their loss sets the tone for the corporations in the long run. Just as how defending free speech for individuals can see you defending hate speech, it seems (to me) like defending cryptobros is better than the alternative erosion of corporations standing up for individual rights.
Biting the hand that feeds IT
