The question -- "how does Sir Thomas More lose the esteem of his colleagues by staying loyal to his conscience?" -- answers itself: More stayed true to himself and his beliefs rather than shift with the prevailing winds of the time. The reason individuals like Sir Thomas More remain part of the public consciousness is precisely for their unwillingness to sacrifice their beliefs for reasons of political expediency.
Robert Bolt's play, made into the 1966 film of the same title, portrays Thomas More as a paragon of virtue, probably exceeding the reality. In relative terms, however, More can be considered a man above his times. The personal courage involved in going against King Henry VIII of England, in a time when total power rested with the throne, was tremendous. Politically motivated violence was quite common in that era, as in others, and the simple and profitable decision would have involved agreeing to support the king's desire to attain a divorce from Catherin of Aragon. By following his conscience, More not only angered the king, but also alienated himself from the king's Court, including powerful figures like Cardinal Wolsey and Thomas Cromwell.