I'm currently looking into the advantages of using Backbone.js, but I'll be using ASP.Net MVC as the main bulk of the site. My question is, is it worth blending the 2 together or am I making a rod for my own back? Should I just use an ASP.Net Web Forms site instead?
Not unless you have strict deadlines or other limitations. It's always worthwhile investing time and resources in better technologies like ASP.NET MVC.
As for using backbone.js it will work with any REST API. You can expose a REST API with ASP.NET MVC (and it's a lot easier to do then using ASP.NET winforms)
As long as you expose your data as a service backbone can work with it nicely. Alternatively you can use ASP.NET MVC on it's own and not make use of the client-side MVC backbone offers.
As mentioned if you just use ASP.NET MVC to expose data as an REST API then this is fine. If you use ASP.NET MVC to serve an entire website (including server-side views) then you'll have a lot of code duplication.
However if your using backbone.js I would recommend you couple it with node.js to minimize code duplication or couchapp to remove the server-side stack. You don't really need .NET if your using backbone.