The term "non-lethal" in general is a misnomer anyway, given that there is no 100% guaranteed safe way to knock out any given person one might encounter under any given circumstances. Granted, some are less dangerous than others, but some are less likely to incapacitate their targets, too.
That noted (for it is definitely worth noting), this is video game logic. All the same, some of the non-lethal takedowns in Deus Ex: Human Revolution seem particularly brutal. I believe that Jensen can reliably KO someone with a single punch to the face with his robot arms, but I'm less convinced that someone could do that with the certainty that it would not do more harm than that.
Then there are takedowns where it seems like they should be able to recover far more quickly than they do. Maybe they don't find that sporting? "No. Jensen flipped me onto my back fair and square. I refuse to take action again until one of my co-workers taps me back in."