consulta recursiva SQL

Simplemente intercambie los campos en la cláusula de unión:

WITH CategoryTree AS
        (
        SELECT  *, 0 AS Generation    
        FROM    dbo.Category
        WHERE   CategoryName = 'Animation'
        UNION ALL
        SELECT  Cat.*, Generation + 1    
        FROM    CategoryTree
        JOIN    dbo.Category AS Cat
        ON      Cat.Id = CategoryTree.CategoryMaster
        )
SELECT  *
FROM    CategoryTree