The current guidelines for the steroid problem are indeed toothless. However, it was/is at least a beginning to addressing the problem, instead of the perpetual blind eye policy that was in place prior to the CBA.
I recall reading that "athletes" were identified by name in files at Bond's trainer's residence. So there is some truth to that story. I don't believe Bonds, nor any individual athlete was identified. However, since Bonds did deny using while testifying to the grand jury, and it is proven that he did use, then he will also face charges of perjury in addition to any sunstance related charges.
I don't believe MLB will be able to keep this mess swept under the rug.