Here's something that works, but it's pretty ugly with lots of if() statements. If I had more time I would do it differently and make it much more compact.

It assumes quite a bit regarding how your code is lined up. The <%-- and --> MUST be on the same line as the <script> and </script> tags, and said tags must be the only thing on the line (and must be in the file's first column). If this is not how your code is consistently lined up, it will not work, but hopefully it is a decent enough example to get you started:

#!/usr/bin/perl

use warnings;
use strict;

open my $fh, '<', 'file.aspx' or die "Can't open the damn file for rea
+ding!: $!";

my @file_content;

while ( my $line = <$fh> ){
    chomp $line;

    if ( $line =~ /^<script>/ ){
        $line = "<%-- $line";
        push @file_content, "$line\n";
        next;
    }
    elsif ( $line =~ /^<\/script>$/ ){
        $line .= " -->";
        push @file_content, "$line\n";
        next;
   }
    elsif ( $line =~ /^<%--\s+<script>/ ){
        $line =~ s/^<%--\s+//;
        push @file_content, "$line\n";
        next;
    }
    elsif ( $line =~ /^<\/script>\s+-->/ ){
        $line =~ s/\s+-->//;
        push @file_content, "$line\n";
        next;
  }
    push @file_content, "$line\n";
}

close $fh;

open $fh, '>', 'file.aspx' or die "Can't open the damned file for writ
+ing: $!";
print $fh @file_content;
close $fh;
[download]

The file I used had these contents:

<script>
</script>

<%-- <script>
</script> -->
[download]