Для чего это стоит, вот как это просто в NumPy:
>>> a = numpy.arange(36).reshape(6, 6)
>>> a
array([[ 0, 1, 2, 3, 4, 5],
[ 6, 7, 8, 9, 10, 11],
[12, 13, 14, 15, 16, 17],
[18, 19, 20, 21, 22, 23],
[24, 25, 26, 27, 28, 29],
[30, 31, 32, 33, 34, 35]])
>>> block3 = a[3:6, 0:3]
>>> block3[:] = numpy.rot90(block3, 1).copy()
>>> a
array([[ 0, 1, 2, 3, 4, 5],
[ 6, 7, 8, 9, 10, 11],
[12, 13, 14, 15, 16, 17],
[20, 26, 32, 21, 22, 23],
[26, 25, 31, 27, 28, 29],
[20, 26, 20, 33, 34, 35]])