It is important to note that the Lord's first clear instruction to Alma deals with repentance.
The Lord makes repentance possible, and stands waiting to forgive us if we will turn to him. Therefore he first provides for those whose hearts may be touched and who are able to turn to him. These people will be accepted into the church (and the covenant) and they shall be forgiven (because baptism is part of the their covenant upon joining with the church).