Is the a way to run a workout along with the navigation?

Very easily. Simply load the course as you would normally, select Home, and load your chosen workout as you would normally. The two will run together - one doesn't cancel the other. 

I don't normally use the unit's own course creation facility to do this; rather, I design my own courses (I tend to find that it's important to consider roughly where one is going to be for each interval - it's not ideal to be starting a five-minute VO2 max interval on a long descent, or in a town street with traffic lights and other obstacles, for example). However, I've just tried what you describe on my device, and it works in exactly the same way.

In fact, I agree with you - I've only recently switched to a 1040 from an old 1000, and would never, ever have trusted that to plan anything more than a very short journey - when I experimented in known areas, the courses it designed were bizzare. The 1040, on the strength of one short experiment, looks considerably better (and also much better than Connect). On this device, it's a function I'd be comfortable using. 

Do you know how to stop navigating during a workout without stopping the workout? It seems there is one button for both on the dark/tap screen and stopping the workout takes precedence. I haven't found any other way,

It's not something I've tried. Normally, I'd stop navigation from the map page by tapping the map and selecting" stop course" (or whatever the message is). Are you saying that when you do that the only option is to stop the workout? 

Try entering the control loop by swiping down from the top of the page. You should see an entry on one of those pages to stop course.

Yes, the only option there is to stop the workout. However, as aweatherall suggested, if you pull down from the top then you have a screen which provides both options (to stop the workout and to stop navigation).

Thank you aweatherall, that worked indeed.