How can I deny "android:keepScreenOn" to a misbehaving app?
Xposed Module

Since your device is rooted, you could install the Xposed framework and then install a module such as App Settings. It lets you tweak settings for an app. In your case, it lets you tweak whether to keep the screen on or not (according to its page, at least).

The Xposed framework has tons of other modules for tweaking the inner workings of Android.