The browser provides much more control over what's happening than executing the code directly on the OS. You can block JavaScript, you can easily analyze the executed source code before you allow its execution, you can manipulate the page as you see fit, you can use extensions to alter your experience in many other ways, and you get the browser's default security sandboxing stuff that prevents it from accessing external domains, your filesystem, or otherwise interrupting non-browsing related tasks.

It'd be crazy to download a full local client for something as shady as SilkRoad or many other hidden services. The browser is the safest place for that kind of thing.