Of course the likelihood of effectiveness matters. As does the potential harm you're risking. What the article is arguing is that keeping the site up allowed for a much greater distribution of the photos -- to potentially many, many more individuals who continue to elude prosecution, and may continue to spread those photos themselves.
At the time the FBI took over the site, there were 11,000 weekly user logins. During the additional time they ran it, it grew to 50,000 weekly user logins. Out of a potential 50,000 individuals, the FBI is able to prosecute only 186. pavel_lishin is asking a fair question when he wonders if allowing a potential 39,000 additional individuals to download those photos and potentially distribute them elsewhere actually resulted in any additional prosecutions, and if so, is that number worth it compared to the (potentially massive) amount of additional distribution the FBI enabled?