Simply put, Danforth refuses to grant a pardon because he is afraid it will perceived as weakness of the court. Danforth is extremely driven by the sense of prestige and the perception of the court by the citizens of Salem. This can be seen during the trial when Danforth questioned Proctor as to his intent. The idea of subverting the court is something that is unacceptable to Danforth, who is more concerned with the prestige of the court and its appearance of being the arbiter of justice as opposed to any other concerns. Danforth believes that granting pardons would delegitimize the court and lessen its credibility. As Act IV progresses, it becomes evident that the rebellions towards the court in neighboring Andover is a pressing issue in Danforth's mind. To this end, he does not want anything to prevent the court's perception as being able to deliver on its assurances and judgments. In this light, granting a pardon, while it might be more in line with the pursuit of justice, is something that Danforth sees as a potential weakness, and not something that he could embrace.