I am not sure if the alignment object is same as a python iterable array. You can try:

myAligment.sort(key = lambda x : x[column you want to sort by])

If that doesn't work, you can always restructure your alignment into an array of tuples:

newArray = [(x[column you want to sorty by], x) for x in myAlignment]

Then sort by the first element of the tuple which contain data of the column you want to sorty by:

newArray.sort(key = lambda x : x[0])

In Biopython 1.60 or later (due to be released soon), you can give the alignment's sort method a key function argument.