I hope that I have understood you correctly. I believe this behaviour is caused my Sammy.js (which the durandal router is currently based on). The default behaviour of Sammy is to hijack all links and process them as regards to the SPA itself.
I didn't like this behaviour for the website I am working on and needed links to other MVC web pages to be possible from within the SPA. What I really wanted is for regular links to just work and hash links to be interpreted as a link to another view within the SPA. So '/controller/action' would go to another web page and '#moduleId' would go to another durandal V/VM.
I found this Sammy option that works for me and set it in my main.js
// This stops Sammy from hijacking regular links
Sammy.Application.prototype.disable_push_state = true;