SQL Server “cannot perform an aggregate function on an expression containing an aggregate or a subquery”, but Sybase can

One option is to put the subquery in a LEFT JOIN:

select sum ( t.graduates ) - t1.summedGraduates 
from table as t
    left join 
     ( 
        select sum ( graduates ) summedGraduates, id
        from table  
        where group_code not in ('total', 'others' )
        group by id 
    ) t1 on t.id = t1.id
where t.group_code = 'total'
group by t1.summedGraduates 

Perhaps a better option would be to use SUM with CASE:

select sum(case when group_code = 'total' then graduates end) -
    sum(case when group_code not in ('total','others') then graduates end)
from yourtable

SQL Fiddle Demo with both