What about WITH TIES?
SELECT TOP 1 WITH TIES tbl1.* FROM
(SELECT CASE WHEN S.Id IS NOT NULL AND S.Status = 1
AND (S.WebUserId = @WebUserId OR
S.AllowUploads = 1)
THEN 1
ELSE 0 AS [Value]
FROM Sites S
WHERE S.Id = @SiteId) as tbl1
ORDER BY tbl1.[Value]