It looks like you're trying to sort the columns independently, and then recombine them visually.

The following produces the results you desire, although it assumes that the left and right columns are the same length.

#!/usr/bin/perl

use strict;
use warnings;

my (@left, @right);

while(<DATA>) {
    chomp;
    my ($left, $right) = split /,/;
    push(@left, $left);
    push(@right, $right);
}

@left = sort { $a <=> $b } @left;
@right = sort { $a <=> $b } @right;

print "$left[$_],$right[$_]\n" for 0 .. $#left;

__DATA__
10,20 
30,10 
20,70 
70,80 
40,90 
90,100 
50,50
[download]

Hope this helped,
-v.