Untested, but let's go for ease of programming here. The suggestion to use MLDBM is very good, as the error is probably due to storing so much in %main_data.

while(@data = $sth->fetchrow_array()) {
    ($curpidm, $curcrn) = @data[0, 8];

    my $dest = $main_data{$curpidm};

    unless($seen_pidm{$curpidm}) {
        $seen_pidm{$curpidm} = 1;
        push(@pidms, $curpidm);

        @$data{qw( Resd Edlv Styp Degc Majr Egol Aprv TermCodeEff Cipc
+ )} =
            @data[1 .. 7, 14, 15];
    }

    my $crn = $dest->{$curcrn};
    @$crn{ qw( Subj Crs Section Sess CreditHr )} = @data[9 .. 13];

    $dest->{CurHrs} += $data[13];

    unless($seen_crn{$curcrn}) {
        $seen_crn{$curcrn} = 1;
        push(@crns, $curcrn);
    }
}

# probably unnecessary
# $sth->finish();
[download]

If that's not correct syntax, it's pretty close. At least it's shorter.