You do not have to destroy a group if you re-use it later.
Usually you only have to destroy a group when you create one using something like 'All units owned by player'. In this case, the easiest method to destroy it is to make a custom script before creating the group: set bj_wantDestroyGroup = true.
If you are only adding, removing, and clearing units from a group, you are not creating a new group, so you shouldn't really have to worry about this.