There doesn't seem to be any question in that memo. Actually, these front office memos are more damning than the accusations against particular players because this is management treating substance abuse as normal and trying to figure out whether it benefits them or hurts them.
I don't see how this report can be considered a whitewash. Mitchell seems to give credit to the idea that half the players were doing something improper, he holds management and the union to have avoided confronting the situation, and he names names of people that he doesn't have an airtight case against, which he didn't have to do if he was trying to cover things up.
I can almost understand why the union told people not to cooperate with the investigation, though I think it was a terrible path to take. But whoever urged these guys who now claim to be innocent not to respond to the specific charges that were going to be made against them gave them terrible advice. Worst labor decision since the umpires resigned.