The Lord is commanding Alma to do that which he was hesitant to do. He was placed in a position which required him to pass judgment, and the Lord is encouraging him to fulfill his duty. This is a difficult position for a priesthood leader but he cannot afford to shirk his responsibility.
Harold B. Lee
"Sometimes, too, stake presidents, bishops, and others are so anxious about not offending someone, that they do not confront them when there is serious moral transgression.
"I was in a stake conference recently where one of the bishops frankly stated that he had determined that he would never excommunicate any person no matter what the sin. I told him that if this was his true feeling, then he was in the wrong position as a common judge in Israel. Whenever I have been asked by a bishop or stake president as to how he should handle a given case, I have usually replied that it was his responsibility as a bishop to make that decision and not mine as a General Authority, and that in making his decision he had better be sure that he was right. To be a judge requires spiritual guidance, tact, and wisdom, but it takes courage when action is necessary.
“I do not think such situations call for stake presidents and bishops to be insensitive or militant, but stake presidents and bishops must realize that the gospel is designed to change us all, to make us more like the Master. When we let members lead a double and destructive life, instead of doing them a favor as we suppose, we damage them, sometimes, irreparably. We must let the light of gospel standards shine fully, and not try to deflect the penetrating rays of its standards. The gospel is to save men, not to condemn them, but to save, it is sometimes necessary to confront and to discipline as the Lord has directed us. When individuals are on the wrong path, our task is to redirect them lovingly, and not to watch idly from our vantage point on the straight and narrow path. (69-13)” (The Teachings of Harold B. Lee, pp. 117-8)
Spencer W. Kimball
"By virtue of his call and ordination and setting apart, [the bishop] also becomes a ‘judge in Israel’ and has the responsibility of making many decisions which affect the progress and development of his people. He gives direction to their spiritual activities so that he can give them opportunities for growth, and judge their accomplishments. He decides as to their worthiness and eligibility for certain blessings and privileges. He holds the key to all temples in the world and it is he who must turn that key to open the doors thereof and that they may go through eternal marriage to life eternal.
"He has the keys to the storehouses and must decide if one is eligible through need and worthiness to be given welfare assistance. ...
"Numerous suggestions have come from many sources in the years past that the bishops should be trained in social work to be able to meet the demands of the people in their numerous needs. But the Brethren have never felt that would be the answer.
"In the Church of Jesus Christ, the leaders have no formal academic training for their positions but gain experience through their lifetime, and they depend much upon the Spirit for guidance. ...
“It would be unrealistic and untrue to state that all these young men are perfect men or perfect bishops. They are mortals subject to the whims and weaknesses common to their fellows. They are not all as wise as Solomon. They are not all as personable as President McKay. They are not all as kind as President George Albert Smith was, but as I have known thousands of them personally through a half century and more, I am astounded at the power and strength and dignity and goodness and ability of these young men.” (The Teachings of Spencer W. Kimball, p. 475)