I think this is hardly worth the additional UI complexity for managing the list of excluded resources. The "disable cache" feature is primarily for quickly obtaining realistic network timings rather than help in refreshing recently modified resources -- expire header configuration could be used on the development server for the latter.

From my development experience excluding assets from cache is used really often due to preventing errors related to not refreshed cache. 
Leveraging headers is an option but in my opinion it creates even more hustle. It's really often that as frontend developer you don't have possibility to set them. Moreover it requires additional level for maintenance (dev config vs stage vs prod). I think that Dev Tools is perfect place for frontend developers to manage this.

I have also another scenario which is can happen for everyone. Let imagine that you are out of the office but with pc and really bad internet connection and you need to make bugfix. Then the simplest thing is to enable cache to not speedup fixing with disabled asset on which you're working on.

Regarding UX i had idea that you'll just mark items in Network panel in different color and disable/enable single item by right mouse click (menu with copy as cURL).

I can give you screenshots if you like. 

Sorry for late response, i was offline.