Having tried Solasta EA where they do have a pop-up for reactions, that does works pretty well... yes the flow of combat is disturbed a bit, but it is already a turn-based game, having a popup doesn't really do that much. And i'm sure there are other ways Larian could do it which would be even less intrusive.
In any case they do need to do something along these lines if they want the Paladin's smite to be anywhere near the effectiveness it is in PnP.
