Would something like this suffice? The \m modifier lets the ^ metacharacter match next to a newline in your multiline $line value.

#!/usr/bin/perl

$/ = ";\n";
while (my $line = <DATA> ){
   $line =~ s/^#.*[\n\r]*//gm;
   print "Query: $line" unless $line=~/^\s+$/;
}

__DATA__
# one comment
# two comment
# another comment

insert into table_name values(1, 'testing 1 2 3');
# more comments
insert into table_name values (2, 'test &#149;')
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OUTPUT:

Query: insert into table_name values(1, 'testing 1 2 3');
Query: insert into table_name values (2, 'test •');
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