It is unlikely, by the way, that Hillary Clinton has inclinations to the contrary—and not just because she appreciates Gen. Jones' bureaucratic prowess. Even accepting the critique that she is looking out above all for her own political future and legacy, she has almost certainly read enough history to know that the most renowned secretaries of state are those who lock step with their presidents—and that those who angle in dissent turn out badly.
George Marshall came up with the Marshall Plan, and Dean Acheson did much to carve the NATO alliance and the post-World War II security system, but they succeeded in doing these things because their plans fleshed out and extended President Harry Truman's general inclinations. Cyrus Vance disagreed with President Jimmy Carter, resigned in protest, and disappeared from public view. Colin Powell might have made a great secretary of state under some other president, but he had to be ousted from George W. Bush's administration because his differences over policy had grown too substantial and public; he couldn't be an effective emissary because foreign leaders couldn't be sure whether he was speaking for himself or for the president (and if they thought he was speaking just for himself, they would have dismissed his words as irrelevant, no matter how much they liked him or disliked Bush).
It is hard to imagine that Sen. Clinton isn't fully aware of these dynamics. I have no inside track on her thinking or on the alleged machinations of her inner circle, but it seems clear that, given the rules of seniority, she would have had to wait a long time to gain a leadership position in the Senate; and unless Obama turns out to be a bust as president, she couldn't have another run at the White House for at least eight years, by which time she'd be almost 70. She may simply have calculated that her best prospects and greatest adventures lie in joining Team Obama as a senior subordinate but a subordinate all the same.
And if I'm wrong about this, or if she gradually takes on more manipulative motives, her stiffest obstacle will be, if not Obama himself, then certainly Gen. James Jones.