What caused jefferson and his party to change their approach to governing, what reservations did they have about what they were doing, and how were they able to rationalize this apparent change in program and philosophy?

The presidential crusade of 1800 that hollowed Jefferson and Aaron Burr against John Adams and Charles Cotesworth Pinkney was sharply challenged. Jefferson and Burr had tied for the administration with 73 constituent votes each and thus the sitting House of Representatives, still overwhelmed by Federalists, was called upon to break the gridlock. 
In the midst of restored fears of common war, the House amassed on February 9, 1801, however following a few days of balloting the result was as yet uncertain. At last, on February 17, on the thirty-6th poll, the restriction split and Jefferson was chosen, finishing "the unprofitable challenge" that had "fomented people in general personality" and almost dove the country into struggle.