Looking at your code, here's what I have in mind as a solution

It might not be perfect:

#!/usr/bin/perl
use strict;
use warnings;

# store everything in a hash where ( option  = hash key ) 
my %HASH;
while (<DATA>) {
    chomp;
    my @line = split /:/,$_;
    my $K = shift @line;
    my @V = split /,/ , shift @line; 
    $HASH{$K} = \@V;
}

# options per line 
my $OPTIONS_PER_LINE = 3;

foreach my $C (1..$OPTIONS_PER_LINE) {
    foreach my $i (sort keys %HASH) {
        print $HASH{$i}->[$C-1];
    }
    print "\n";
}

__DATA__
option1:apple,banana,orange
option2:apple,banana,orange
option3:pork,chicken,beef
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