IMO, there are several ways of looking at this. One way to see it, which is possibly the position of the EFF and the sex worker support organizations they cite see this is as an unjust law which amounts to legal but immoral persecution of vulnerable people, prostitutes. Parallels could be a gay dating site in Jamaica or a political dissident forum in China.
From another perspective, it's one of those grey areas where you agree the activity should be illegal but prostitutes should be treated as victims or vulnerable persons.
Parallels to an information site for recreational drug users or a needle exchange. Harm reduction instead of law enforcement. Association is important here.
This represents a loss of a resource which provides them support and helps them bring down their risk of harm. More worringly, it's bullying. Creating a fear of that any associations will be persecuted.
From the perspective most natural to the EFF, the problem is exposing everyone because a few are suspected of criminal activity. Not all sex workers are criminals. But because some (allegedly) criminal activities happened on the site, everyone associated with it is compromised.
All together, this amounts to tactics fro preventing free association and speech. It's staring off by targeting a group that no few will openly defend, prostitutes.
I personally am sympathetic to all these views. I think prostitution (to the extent that it is consensual) should be legal. I think that if it is to be illegal harm reduction is much more important than enforcement. Arresting prostitutes is like jail-time for illiteracy.
The most scary thing out of all of this is the exposure of anyone and everyone that has visited or registered on these site. It starts with some marginal group where many/most are breaking the law, some are breaking the law on the site and everyone is marginalized by society. From there we gradually get to a situation where any online criminality leads to massive data seizure and exposure of anyone associated with the site.
Logged in to a body building site where some people sold steroids on IM, on a list. Commented on a blog discussing civil disobedience where some petrol bomber hung out, on a list.