The idea of a President and his cabinet and/or his Vice President not getting along is really nothing special. We had the 'kitchen cabinet' of Andrew Jackson which led to armed posses and near duels over a woman's honor, we had Thomas Jefferson's service as Vice President to John Adams who felt that he was actively trying to undermine him and today is no different- with the presidential hopefuls John McCain and Sarah Palin who now it seems, could barely stand each other.
That's all normal, but never before the Polk administration did a President have so much animosity towards an active General fighting a war. As General Zachary Taylor, a Whig (not even a declared Whig at that point), was fighting the Mexican War, James Polk, a democrat, did everything that he could to minimize his victories on the field of battle so he couldn't become another War Hero president like Henry Harrison.
Polk was like a less corrupt Richard Nixon, brilliant and effective, but thinking that everyone was out to get him. By the time of his administration, the Whigs blossomed into an effective national protest movement against the Democratic policies of national expansion and limited 'internal improvements' Polk espoused. He constantly wrote to friends, suspecting Taylor of 'Whiggery'.
The irony of this strained relationship, is that Taylor was more or less completely apolitical until the Whigs convinced him to accept the presidential ticket in the election of 1848. Once he accepted the nomination as Whig candidate, he refused even to put his beliefs in writing, simply saying that he'd 'protect and enforce the constitution'. I think that Taylor's limpness on issues hardly put him in the category of Whig crusader.
Imagine today if President Obama kept General Gates' from enacting his policies to keep him out of presidential contention. How would the American people feel about that?