I have found it simplifies deployment to have the website project contain only content (no compiled code).
Something like:
Web.Site project
Content
Images
Css
Scripts
Views
web.config
And move all compiled code into another project:
Web project
Controllers
Filters
Models
...
Then, you can treat everything within the Web.Site project as needing to be deployed, and all required assemblies will be in Web.Site\bin.
Whether you are doing simple xcopy deployment, or using WiX to build an MSI package, this will make life a little easier.