Dano - your point kind of re- inforces something I said in another post. LEOs are always going to be subject to this kind of situation unless there is a clear way to prove that it is not the case.
Pepsi was able to quickly clear its name from a false "something is in my can of Pepsi" a few years ago, because it had done such a good job, over a long period of time, of making sure its systems and practices were broadly judged by the general public (and expert analyst) as sound, safe, and logical. Many people have seen Pepsi being made and bottled / canned, and feel much more comfortable about the probability of it being "good" as a result.
Most police agencies do not have a strong, independent, citizen based, equivalent of this kind of quality control. Instead, they rely on "internal experts", who the public may or may not believe. (If you need an example of what the public really thinks of "internal controls" - think Enron and Tyco )
While important for public relations, an elementary grade schol tour of the local Police / Fire Station does not fill this gap. The SF PD did not help itself in this area, when it apparently did not provide even basic responses to the appointed citizen review board requests.
I am not saying anyone there is doing anything wrong, but the fact that they "appear" to be doing something wrong is actually worse, because it enables articles like this, factual or not, to be taken as "likely". Once our public safety officers embrace strong, independent, citizen oversite, the number of articles like this will rapidly decline, as the content will loose its potential to cause a sensation.