I take away a slightly different point of view - I really don't believe J actually knew anything about what was going on based on first hand observation (i.e., whatever suspicions he had was all based on second hand info reported to him by the "source") until he offered amnesty to those who admitted their involvement - and from that point on all of the info he had came at the price of his own promise. I don't believe he is withholding the info he obtained to "protect" anyone, I believe he is protecting his own honor by living up to his promise. Subtle distinction - but significant, IMO. (I think anyone reading this who is Catholic - and has gone to Confession - understands the significance of this)
Interesting, too, that in his own letter of response, J seems to indicate he understood that his promise of "amnesty" was not, in his view, binding on the administration (i.e., did not guarantee the culprits legal immunity); rather, it was on the information that he obtained confidentially that he alone was responsible for honoring his pledge.
Ironic, I think, that if J had simply reported the allegations to his superiors (in which case they would have known nothing further than what they now know), and then did nothing, he may have been better off.