Как насчет того, что вроде
chosen = (1, 2)
right_down = chosen[0] + 1, chosen[1] + 1
matrix[chosen], matrix[right_down] = matrix[right_down], matrix[chosen]
выведет:
>>> 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]])
>>> index = (1, 2)
>>> right_down = index[0] + 1, index[1] + 1
>>> a[index], a[right_down] = a[right_down], a[index]
>>> a
array([[ 0, 1, 2, 3, 4],
[ 5, 6, 13, 8, 9],
[10, 11, 12, 7, 14],
[15, 16, 17, 18, 19],
[20, 21, 22, 23, 24]])
Должна быть проверка границ, но она опущена