What should an imam who received a salary for five years for leading prayers at Al-Mahatta Mosque without actually leading the people do to atone for these salaries and have his repentance accepted by Allah?

Your friend does not deserve the Imam's salary as long as he has not led the people in prayer. He must return what he took as salary for the past five years. He must also fulfill the conditions of repentance: regret, cessation of the sin, and determination not to return to it. He should also increase his seeking of forgiveness.