There are better ways. Rather than write to a file, you could create a script tag that points to a server page that generates the script like this:
<script type="text/javascript" src="GenerateScript.ashx"></script>
<script type="text/javascript">
// write some page level code here
</script>
Make sure you test in a few browsers because some may cache the dynamic script. You can also pass parameters to your handler:
<script type="text/javascript" src="GenerateScript.ashx?x=1&y=2"></script>
<script type="text/javascript">
// write some page level code here
</script>