I am using Visual Studio 2010 and using web deployment to promote the .Net MVC site to specific environments. I installed Elmah, and it worked great on my DEV environment, but
I think Visual Studio will detect that SQLite is required by Elmah and copy it if it finds it. In order to achive the same goal as you I removed all SQLite stuff from the Elmah source code and re-built it. It is quite painless thing to do...