The politics of these two groups are very related -- enemies are incredibly joined in politics. If Group A gains power by being against group B, then I _must_ be allowed to talk about the failings of group A -- your attempt to portray that as not allowed is incredibly damaging.
Reactions like yours about "distastefulness" has been the problem with the counterterrorism movement from the very beginning. Counterterrorism is a movement that works like this: there exists a group B of pure evil, they must be fought and opposed, group B is shadowy, includes small numbers of people, and the people who are in it are very similar to much larger groups not in B. This is a priori accepted -- any attempt to disagree with any of the above comments is working against counterterrorism.
What this environment causes is a very real perceived expansion of group B in the eyes of members of group A. It becomes a simple mechanism for leaders of group A to use their relationship to group B to remove any legitimate political voice from other groups C,D...
It is completely fair (and needed) to talk about the flaws of group A's behavior with regard to the concept of group B because the accepted concept of group B includes primarily people who are not in group B! Not doing this has already killed huge numbers of innocent people not in group B. It's sick and it's wrong. It was sick under Obama and it's still sick and wrong.