SQLite doesn't do the full outer join thing, so you have to fake it with two left outer joins :

-- in table2 but not in table1:
SELECT r.id
FROM table2 AS r
LEFT JOIN table1 AS l
  ON r.id = l.id
WHERE
       r.system = ?
   and l.id IS NULL
   and r.id IS NOT NULL

-- in table1 but not in table2:
SELECT l.id
FROM table2 AS l
LEFT JOIN table1 AS r
  ON l.id = r.id
WHERE
       l.system = ?
   and l.id IS NOT NULL
   and r.id IS NULL
SQL
[download]

But other than that, SQLite is up to the task, as it includes a nice bulk import statement (SQLite 2.x) and a bulk loader program (SQLite 3.x).

Update: Added the "full" to "full outer join", as a "left (outer) join" is an outer join too, but one which SQLite does...