You say it is hard, and I kind of agree, as especially in narrative-driven games you have to keep a tight rein on things or the structure of the game will be ruined, but this 'killed by game' mechanic is something I have only noticed creep in to games recently tbh, especially from Ubisoft and Naughty Dog. It was really AC3 then 4 that I began getting annoyed by it, then it even crept in to the Splinter Cell series, which had managed fine without it for long enough. Before this, I am struggling to think of many games that did it really.
For Watch Dogs as an example, I think the third mission, where you are taking a car somewhere and you are trying to evade the cops, if they spot you its game over...I don't understand why you don't get the chance to try and outrun them! And as for the Gang Hideout missions, it is particularly strange imo as they are optional sidequests, where it really doesn't matter in terms of story whether you kill him/fail or not, so there really is no reason to force a particular outcome.