Not sure if this is much better than your code:

#! perl -slw
use strict;

my %invert; @invert{ qw[ A C G T ] } = qw[ T G C A ];

my $in = do{ local $/; <DATA> };
chomp $in;
print $in;

for my $p1 ( 1 .. length( $in ) -2 ) {
    next unless substr( $in, $p1, 1 ) eq $invert{ substr $in, $p1+1, 1
+ };
    my $pals = 0;
    for my $p2 ( 1 .. $p1 -1 ) {
        last unless substr( $in, $p1-$p2, 1 ) eq $invert{ substr $in, 
+$p1+$p2+1, 1 };
        ++$pals;
    }
    if( $pals ) {
        printf "%s%s at %d\n", ' 'x($p1-$pals),
            substr( $in, $p1-$pals, ($pals+1)*2 ), $p1-$pals;
    }
}

__DATA__
AGAGGTCAGTCTGCATCGTATCGATCGTCGACGATCGATACGATGCAGACTGACGAGAG
[download]

Produces:

[13:44:54.28] C:\test>1085446
AGAGGTCAGTCTGCATCGTATCGATCGTCGACGATCGATACGATGCAGACTGACGAGAG
           TGCA at 11
                   ATCGAT at 19
                     CGATCG at 21
    GTCAGTCTGCATCGTATCGATCGTCGACGATCGATACGATGCAGACTGAC at 4
                               CGATCG at 31
                                 ATCGAT at 33
                                           TGCA at 43
[download]

Modify to taste :)