I know I can do it in IIS Manager, but I am looking for some programmatic way to do it. We need to do this for customer all the time. So it would be great if there's a programmatic way of doing so.
There isn't a reliable programmatic way to automatically convert .htaccess files to web.config files because IIS's configuration is quite different from Apache's, as well as their configuration file formats.
There are some sites which claim to do automatic conversions, but the scope and accuracy of these are questionable.
You can however suggest that your client add an IIS module that uses standard regular expressions, since Apache's mod_rewrite module uses Perl Compatible Regular Expression vocabulary - see: Apache - mod_rewrite-Regular Expressions
One such module is ISAPI_Rewrite, which is written in pure C/C++. From their FAQ's:
Using regular expressions for IIS should help to greatly speedup conversions of Apache RewriteRule's.