I've done this trick on my last playthrough, smashing the wall and knocking out the person on the other side.
As I expected, I got Pacifist at the end.
So, in short, no, this technique does not disqualify you for Pacifist.
That said, the criteria for Pacifist are quite weird, I think the game is designed to be lenient.
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What you can do (instead of wall punching) is to use a revolver with explosive bullets on the wall.
It will render the person on the other side unconscious when the wall breaks, instead of killing him (2 rounds AFAIK).
It made the Tracer Tong mission extremely easy (playing non-lethal).
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After taking the wall breaking perk, I found myself in the situation of breaking through walls leading the lethal deaths.
I noticed that the wall had a health rating, like crates do, taking a indestructible object, a barrel, I threw it against the wall multiple times
until it broke, this alerted the guards but this method works without any expenditure of grenades or explosive shots from a revolver.
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If you don't have a revolver with explosive bullets, you can also toss a frag grenade at the wall.
The wall will come down, but the person on the other side will only be knocked unconscious.
gaming.stackexchange.com/users/5398/Steve V.
You don't need explosives.
It takes a few shots
but I was able to break through a wall with my silenced 10mm pistol.
I do however have the armor piercing on it
but I tried it with my shotgun(not modded) and after about 5 shots I broke through.
It did a non lethal knockout on the guy on the other side of wall for those pacifists out there.
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So the wall-punching augmentation (in the Cybernetic Arm Prosthesis augmentation tree) allows you to punch through weak walls, but will automatically have you snap the neck of anyone standing on the other side of them.  Am I correct in assuming this will ruin a pacifist playthrough?  Is there any way to do a non-lethal wall-punch and only snap his neck a little bit?
How can I not snap people's necks (or only snap it a little bit)?
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<deus-ex-human-revolution>
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gaming.stackexchange.com/users/7816/Ian Pugsley
This does not disqualify you as a pacifist. Try tossing a frag. The wall will come down but the person on the other side will only be knocked unconscious. Several techniques can be used in order to do a non-lethal wall punch and it does not disqualify a player from doing a pacifist walkthrough
Breaking a wall and knocking out the person on the other side does not ruin a pacifist walkthrough There is a variety of techniques to break a wall in order to knock out the person on the other side