I'm inclined to think that anything that went from the FBI to Twitter went through Twitter's Legal Department, and at least one person signed off—which, given the rebuffs of more public attempts, seems like anything signed off on was done in good faith. So in my mind the problem isn't Twitter, it's the FBI. To me it's the framing (which was always going to be problematic, it's Matt Taibbi).
And to be clear, I think one isn't paying attention if they try to lay blame at the feet of any one administration for this, this is a long-standing issue originating inside the FBI.