We don't know all of the specifics here, but for the feds to go after it one must assume that there was mens rea for the underlying offense (i.e., the hackers were in fact black hat) and there was actual harm (i.e., the hackers kept the stolen data and either intended to or did in fact use it for criminal purposes).
And in order to go after charges of obstruction and misprision, the DoJ must also believe that Sullivan was clearly aware that this behavior was criminal, and he intentionally sought to cover it up. This isn't much of a stretch because the FTC was probing it, so there was ample opportunity for him to respond incorrectly (and, allegedly, criminally) to FTC's questions during their probe.