Don't get me wrong, I like to play on the "shady side of neutral" from time to time as much as the next gamer. My group has done this several times, with the whole group in agreement, but it is not our default.
I think if we were to do it consistently, it would grow tiresome. Most of the players in my group's "normal" parties seldom take a black-and-white view of good and evil, and I get the whole "adapting to the group's whim" thing, but are they seriously like that all the time?
Not the entire group, nor all the time. A few players play characters with a more "anti-hero" mindset. That it's never ok to let a villain or enemy escape, in case they come back to haunt the party later; that force is the most effective form of interrogation, etc... Basically more of a Punisher type character than Spider-Man (to use a comic analogy).
This last campaign we've been playing (Eberron with a focus on urban intrigue) has been a bit more in this style which is why it's more in the forefront of my mind. An example: when some cultists that were mentally/spiritually possessed by a creature from Khyber attacked the party, they killed most, captured two for questioning. The questioning soon turned to interrogation and torture, with hands and feet being amputated. Of course the party's guide fled in utter horror at what he witnessed. One party member objected to the amputation/torture, but when she went after the guide (to try and calm him down), the prisoners ended up in a nearby lava pit.
It was the kind of situation this article would have tried to address. The villains were beaten, and once the mental domination had weakened, surrendered. It was going to end up in a skill challenge to get some info from the prisoners, but once the torture began, I pretty much let them know this wasn't going to get anything useful.
I'd be curious to see how the party would react with a reversed role; especially considering in our last session, the party psion was captured by a group of mercenaries. This was a perfect example of where a fight/flight situation occurred. The psion was alone, against two of the mercenaries. Had he tried to flee, it could have been resolved in a skill challenge. Of course, the character stood his ground and was eventually knocked unconscious.
Had this kind of rule been part of the group's normal bag of tricks, I wonder if it would have gone down differently.