I feel Deus Ex: Human Revolution also fell prey to this dual gameplay ideology, especially since it's an RPG. Sure, you can shoot your way through, but non-lethal silent takedown gives 40 xp, headshot kill 20 xp, normal kill 10 xp. This gears one mechanically towards stealth play-style. Hacking also provides additional experience, but requires big xp investment to open it up fully, therefore you have to be stealthy to get to hacking. Narratively one is also pushed towards stealth, because more experience means hacking which in turn means more details about the world.
Unless it was a scripted sequence (sniping around helicopter), getting shooty always felt like a fuck-up. And another problem is that while going from stealth to shooting was not that difficult due to weapon upgrades, going the other way mid-game would be nearly impossible due to insufficient xp pool and non-optimal skill selection.