use strict;

my $delim = $/;
$/ = '';
my $file = <DATA>;
$/ = $delim;

$file =~ s/(<%--)?\s*<script(.*)>/($1 ? '' : '<%-- ') . "<script$2>"/ige;
$file =~ s=</script>\s*(-->)?='</script>' . ($1 ? '' : " -->\n")=ige;

print $file;

__DATA__
<script type="java/js">
foobie bletch
</script>
<%-- <script>
zelgo mer
</script> -->