I have a standard ASP.NET MVC (version 2 preview 2) solution with the actual project and server-side unit tests in separate projects.
Because this project is very clie
It's not too clear to me why using MVC makes a difference - if you want to integrate your tests into a CI build then gWiz's suggestion is the route to go.
If your requirement is that you want to run your tests interactively directly on the real page without affecting the look of that page then you could check out the FireUnit plugin for Firebug. You can also wrap FireUnit around QUnit as described on John Resig's blog.
If you're concerned about including test stuff then include the relevant scripts in your test/debug builds and disable/remove them in your production builds.