Recall how intimately Obama involved himself in many killings:
President Obama, overseeing the regular Tuesday counterterrorism meeting of two dozen security officials in the White House Situation Room, took a moment to study the faces .... Mr. Obama has placed himself at the helm of a top secret “nominations” process to designate terrorists for kill or capture, of which the capture part has become largely theoretical.
And the central a role Brennan played:
Beside the president at every step is his counterterrorism adviser, John O. Brennan, who is variously compared by colleagues to a dogged police detective, tracking terrorists from his cavelike office in the White House basement, or a priest whose blessing has become indispensable to Mr. Obama...
Finally, recall the chilling logic these two settled on:
Mr. Obama embraced a disputed method for counting civilian casualties that did little to box him in. It in effect counts all military-age males in a strike zone as combatants, according to several administration officials, unless there is explicit intelligence posthumously proving them innocent.
Even if Brennan told everything he knew, I'd still guess that the odds would be heavily against Obama ever finding himself on trial for civil-rights violations or war crimes (though if I were Obama, I'd take proactive steps to lessen the odds further.)
But I can imagine details that could cause Obama's image to suffer, now and in the eyes of history. He might be subject to travel bans or indictments in absentia in certain countries, for example. We don't now know what sort of legal authority Obama had the first time he ordered Anwar al-Awlaki to be killed, or why his 16-year-old son, an innocent American teenager searching abroad for his absentee father, ended up dead. There's still much classified information about innocent people killed in drone strikes.
I am not suggesting that Brennan is blackmailing Obama, or even that he would necessarily retaliate if fired. Still, if Obama is like most people in positions of power, he fires no subordinate without first asking himself, "Could this person damage me?" If Obama is a normal person, rather than an unusually principled person, the answer factors into his decision. Look at what Brennan said in March, immediately after denying that the CIA spied on the Senate Intelligence Committee, when Andrea Mitchell asked if he'd resign his post if that turned out to be wrong:
... if I did something wrong, I will go to the president, and I will explain to him exactly what I did, and what the findings were. And he is the one who can ask me to stay or to go.
He's a smart man.
All this may be irrelevant to his continued tenure. Perhaps Obama has always believed and continues to believe that Brennan is doing a heckuva job. But just as secret torture acted as a cancer on the U.S. government, encompassing acts so barbaric and criminal that, even recently, the CIA spied on a Senate subcommittee investigating the subject, America's semi-secret policy of semi-targeted killing rendered everyone involved complicit in activities sufficiently dubious that all desire their secrecy. Would you fire a guy who knows as much about your most morally fraught acts as Brennan knows about who Obama has killed in secret? Yeah, me neither. This isn't the biggest cost of presidents who hide arguably illegal actions by declaring them state secrets. But it is certainly one of the costs.