Yet another reason why I lay awake at night seriously considering throwing out the D&D alignment system altogether.
Hmmm... so much to discuss. Let's start with what I believe is the major issue as it relates to the game. The DM and his "call" about the subdual damage. It's been repeaded here already, several times, but the fact is that the DM made a bad call possibly motivated by selfish reasons. A critical strike on a subdual attack does NOT mean you accidentaly do lethal damage to your target. The d20 system of Task Resolution is set up so that the higher the roll, the more favorable the result is to the person who rolled. This BS call by the DM, quite frankly, makes me sick. If he honestly didn't understand the rules, then he should apologize to the players. If he did this deliberately to turn an already bad situation into a complete SNAFU then he shouldn't be DMing. The rules exist for a reason, so if you choose to meddle in them this way you'd better have a damn good reason why.
Now, onto the character's actions. There are at least two scenarios that are possibly relevant. Scenario one; the PC's decide on this course of action immediately after hearing about their comerade's imprisonment. If this is the case, then the alignments of the PC's should definitely shift away from the "good" and "lawful" axis unless they were already mostly neutral or evil to begin with (which could be the case). They didn't even consider any other alternatives that may have worked, so they are totally responsible for their own stupid actions.
Scenario two; the PC's had already tried several means of releasing their theifly friend and none of them worked. Therefore, they devise this hairbrained scheme to force the Rogues release from prison. Now, if for some reason the heroes were about to embark on a quest of Immense Importance for the Good of the Realm (TM), I might be able to see them doing this because of the "Needs of the Many" argument but it would still have an adverse effect on their alignment. Even if this was the case, they would have been better off just trying to break their friend out of jail the old fashioned way.
So you see there are a few things about this situation where clarification is called for. Based on the rather limited description given of the scenario, I'd say that the PC's just came up with this "brilliant" plan on the fly and hoped it would work. If that's the case, then you bet their alignments (if lawful and/or good) should shift. Granted, this is hardly what I'd consider to be the Paragon of Evil Acts but it's still very un-kosher unless the PC's were an unscrupulous lot to begin with. The game is still very salvageable and I think that it will make for some great rp-fodder in the future.
I also see that some of the discussion has touched on the "Evil for Greater Good" idea and the concept of the "Road to Hell being paved with good intentions." Well, let me ask all of you this.
If the Supreme Being of the Universe (God, Allah, whatever) came to you and said, "I hereby give you the moral authority to make this decision. You can put a stop to the violence and hatred that permeates mankind, virtually ending all warfare, but you must kill one innocent man to do it."
Would you? Just curious.