I think you will have to refactor some things. It's difficult for us to know where it will be the most appropriate without being at your seat :-) For example, adding a try catch to all finalizers does not seem a so big deal to me (you can search finalizers using a regex for example), but it may be to you.

The .NET Framework really assumes that the assemblies you reference and the types you use are there at runtime. If you want a more dynamic system, a plugin-type architecture, you need to architect your assembly and your types differently for example using things like the System.Addin namespace or other libraries such as MEF (see this on SO: Choosing between MEF and MAF (System.AddIn))

So, in your case, you could solve the issue in Foo like this:

public class Foo : IDisposable
{
    // use another specific interface here, like some IBar,
    // this is a sample, so I use IDisposable which I know is implemented by Bar
    private readonly IDisposable external;
    public Foo()
    {
        Console.WriteLine("Foo");
        external = Activator.CreateInstance(Type.GetType("AssemblyB.Bar, AssemblyB")) as IDisposable;
    }

    ... same code    
}

But that means refactoring too...