This is exactly why I support the ACLU. It views the law very clearly, and does not deviate from that view at all. They do not defend people or organizations based on values or appearences. They take on cases based on the legal stance of the case itself, not the actual parties to the case.
In the first example, the case against NAMBLA, it is very important to see what they are defending the organization from and why.
This is not a case against NAMBLA in regards to whether or not the information on their website is legal. It is a case arguing that they have criminal fault in the Curley's case. This is similar to:
Suing McDonalds for making people fat.
Suting Gun makers for murders commited with their guns.
Regardless of the outlandishness of NAMBLA, they are not responsible for the acts of the Curleys.
In the second case, with the Boy Scouts. It's much of the same. The ACLU has a view on seperation of church and state, and the situation with the Boy Scouts violated it. They aren't saying that the Boy Scouts were in anyway doing a diservice, but seperation of church and state does not come with a gray area.
I can see where people construct these situations into attacks they are not. Bill "Sexual Harrasment" O'reilly does people a disservice by mudding the waters instead of explaining the justification for these cases.
It's not about the organizations, it's about the law.