The easiest way right now is to toggle the Hue setting in Options - f.lux won't forget credentials so it is easy to turn back on. We could move this up somewhere to the Hue menu so you can get to it easier.
Regarding why disable isn't linked: We think of this as a "home controller" and not a "light near my computer" controller. If you have 20 hue lights and you alt-tab to Photoshop it is too much if your whole house goes to daylight...