1. Create ColdFusion based web services
2. If you have existing pages that take HTML form data via HTTP posts to make the API changes you want, just post to those pages from your .NET application.
Generally speaking the way to talk to a CF application from .NET is webservices.
With what I know about cPanel I presume that you specifically want to talk to Admin API: http://help.adobe.com/en_US/ColdFusion/9.0/Admin/WSc3ff6d0ea77859461172e0811cbf364104-7fcf .html
The Admin API offers access to all the ColdFusion administration functionality and is a stable API. Even if the internals of ColdFusion change, Adobe will try to keep the API the same. The problem you will have is accessing this API from .NET. All the methods in the API are exposed as "public" methods allowing them to be accessed from CF, but not as "remote" methods, allowing access through the webservices. So what you probably need to do is write a small wrapper class to extend the existing CFCs in the administrator and makes them accessible through webservices and then invoke this wrapper from .NET.
Thanks for your help. I have done additional research in this area and feel your suggestion is the best, and perhaps the only, way to do what we need.