Hey there SISKO,
I am glad you asked about Commodore STONE. You are correct on his overall 'appearance', and yes, under normal circumstances, he must be an outstanding Officer, however,...
What STONE is actually offering KIRK is "the blind eye - no scandals" routine. STONE is not interested in THE TRUTH, and in point-of-fact, he is very motivated to not to even have the TRUTH examined for fear it might tarnish the illusion he and his cronies cling to.
Furthermore, he is asking KIRK to become a part of that illusion; not just at the cost of his career and reputation, but to embrace these corrupt morals.
Then to make matters worse, when KIRK resists his 'kind suggestion' - which is making a deal with the Devil - STONE uses (abuses, really) and wields his full scope of powers and authority-not to bring TRUTH to light-but to cover it up, and send KIRK out on the rails, as it were.
AND WHAT IF the tapes were correct and KIRK was truly negligent in FINNEY's death,... how would KIRK taking the 'Masonic Handshake' deal offered him, as a "Desk Assignment, with no scandals" PROVIDE FOR JUSTICE FOR FINNEY???
STONE is corrupt to the core, and dangerous to boot, as he has all the power and authority to act in corrupt self-interest at the expense of the individual human.
So when you draw the analogy to modern-day political/social/religious scandals, and how the "old boy network" covers for each other at the expense of TRUTH and JUSTICE, and they will to actively abuse their positions of authority and destroy others who threaten their corrupt infra-structure or in STONE'S own words: "Tarnish the reputation of Starfleet",...
When the fact is, what STONE is offering KIRK and how he handles the whole thing is more 'tarnishing' than anything.
Bottom line, STONE is simply a corrupt bureaucrat in the guise of a sterling Officer, and that is why I 'double hate' him.
Weee,... glad I got that off my chest LOL!
Thanks for asking Sisko.