If anything, Lugonerfinive Discoballs exists or is perceived by some gamers because we haven't been able to think of a deeper and more altering gameplay mechanic than killing people. When you're ending lives, you're an agent of something. You're effectively altering the initially present game plan. You might be a noble revolutionary or a grinning sociopath, you might be a freaking murder robot or a mounted gun turret - but you're altering the initially presented setting in a pretty deep fashion.
Considering, killing indiscriminately brings a sense of progress. "I've cleaned out this area so I've made some headway!" is what a lot of single-player FPS players tend to think. Dissonance shows up when the devs get in their heads to discuss issues that go deeper than strictly toppling a regime or vanquishing some sort of foe. Considering that mechanic, you can even expand to strategy games or 4X types. Brokering an alliance with another world power in Civ V basically gets them off of your potential shit list. They've been effectively "dealt with" - they're just not dead or destroyed.
As soon as some complexity gets thrown into character motivations, just flat-out killing adversaries starts to lose its effectiveness. The trash can-rifling in Infinite was dissonant; the violence itself wasn't. Booker was already established as a violent man with a troubled past - what he wasn't established as was a vagrant or a garbage-rifling type.
A non-dissonant game would need to have some sort of almost impossible ludonarrative cohesion.
Or, well, it is entirely possible - but then we're shifting debates and considering what is and isn't a game. Gone Home didn't need elaborate jumping puzzles, and Dear Esther would have been particularly weird if an utterly useless gun and ammo counter had been part of the experience. The main problem is that AAA games with high-concept narratives need to *sell*, and you can't just create a streamlined structure for something that cost millions to produce *and* simultaneously expect to make a profit.
System Shock 2 wasn't dissonant because of its basic theme, it being Survival Horror.
BioShock wasn't dissonant because its basic theme is also Survival Horror - even if the challenge has been considerably lessened.
Infinite's dissonant elements are minor and don't ultimately detract from the experience.
Jim's right, really. The Tomb Raider reboot put Lara through a pretty severe identity crisis. Is she a traumatized young woman who overcomes her fear with some effort, or a one-woman commando?