Detect screenshot being taken and disable specific app
It is possible with  Macrodroid automation app (free upto 5 macros) and real easy to learn

I modified a macro to take screenshots on shaking and added your Twilight app 



Shaking the device takes shots (Trigger)

First action is Killing Twilight app ( requires root ) - alarm , pause, take screenshot, pause (adjustable for the time you think you would take a screen shot), launch Twilight app

Constraints -run this macro only when screen is on - so that you don't take screenshots while device is in pocket

After taking the screenshot you will be directed to Twilight page and not the page you were on - you need to switch to previous app

Edit: Here's a gif that shows Twilight being killed, screenshot taken and Twilight enabled on the Macro above

Go ahead and root, if you want this feature !