An alternative to the join's and building the multiple ?'s is using SQL::Abstract:

use SQL::Abstract;
my $SA = SQL::Abstract->new;
while (my @row = $dbq->fetchrow_array) {
  my %fields;
  @fields{@fields} = ( $site_hostname, $site_id, @row );   # hash slic
+e to set %fields
  my ($sql, @bind) = $SA->insert( $thisTable, \%fields );
  push @central_insert, [ $sql, \@bind ];
}
...
$dbh->do( $_->[0], {}, @{$_->[1]} ) for @central_insert;
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In this case, you lose the ability to prepare the statement, but in general SQL::Abstract can be very handy... Good example is with dynamic where clauses.

(i'm also not sure why OP needs to queue up the insert's for later and just doesn't do it in the main loop...)