How about a JOIN by row number?
Something like:
SELECT ...
FROM (SELECT Id, SourceID, [Order], ROW_NUMBER () OVER (ORDER BY [Order] ASC) AS RN FROM Target) t
JOIN (SELECT Id, [Order], ROW_NUMBER () OVER (ORDER BY [Order] ASC) AS RN FROM Source) s
ON t.ID = s.ID AND t.RN != s.RN