If your application is an ASP.NET application, you can effectively script it in C# using the App_Code folder. In the application's folder, create a folder called App_Code and drop a .cs file in there. Any changes to this file will be dynamically compiled by the ASP.NET compiler and result in a restart of the application. This code will have access to all of the assemblies in your app.
To get this code to execute, you can hook up to an application event or you can write a piece of code in your application to dynamically discover and call it, for example by implementing a known interface with an App_Code class and doing an assembly scan for it when your app starts.