Here is the issue. If you believe, as I see it, that particular stumble happened during the final moment before her take off for a Triple Toe Loop, then what consequences it entails, in terms of its gravity or lightness, should not be a consideration. Otherwise, if we let our personal preference color our judgement, then this becomes subjective if not biased judging. Don't get me wrong, I want to stress again the discussion here is purely educational - no one has been cheated and no one is being biased here. We all have our disagreement with the rules and in many ways, the CoP is a good system but far from perfect. But not matter what our personal opinion is re: the system, it has to be followed to the letter for the integrity of the process and fairness to all skaters, from the lowest level to the elite athletes. Yu-Na Kim has her share of run-in with the CoP too, if you recall, her final spin at the 2009 Worlds was voided by Technical Panel, that's about as costly as the value of a Double Axel. Rachael Flatt had one of her spin voided as well at the 2009 Skate America. Numerous other skaters have had their jumps voided, including Asada herself at the Rostelecom Cup 2009 (Russia Grand Prix). Are those mistakes costly? Absolutely! Too harsh or not is not a consideration. So if you accept that her preparation for take-off should be deemed an Attempted Jump as defined in the ISU Technical Handbook for Singles, then the skater needs to be penalized accordingly regardless of how we feel personally.
You raise a lot of good points around the issues...my comment was based on my gut rather than thinking it through, but I guess I'll share where I'm coming from.
First of all, I have no judging experience or even a long-term analytical habit as a fan. I learn selective details at convenient times rather than studying the system for its own end.

I once took a survey course in Philosophy of Law, and some concepts really stood out for me, so I'd like to speak in the abstract with my (imagined) understanding.
I realize that my desire to be forgiving or lenient with Mao Asada (or any skater) needs to be tempered by fairness towards other skaters, as well as by respect for the rules that are in place.
Some rules are in place because they are just good housekeeping; they keep the competition going in an organized way. The time limit rule is one of these. Other rules are in place because the ISU has some sort of philosophy of skating--what it should be, what should be rewarded, what should be discouraged, etc.--that it wants to promote via points or deductions that are allotted for what skaters demonstrate in a competition. The judges (including the technical panel) are supposed to be well-versed in these rules and apply them in a manner that is hopefully fair and consistent, more or less between themselves, and also with themselves (i.e. when they grade different skaters at various competitions.)
You are pointing out that letting Mao off her botched 3T attempt would be inconsistent judging, which is biased and unfair.
There is a set of rules and situations that are extremely clear-cut, black and white, on what needs to be done in judging. However, there are also situations where the rules and judgments are not as clear-cut, and where it is up to the judges to decide how to apply or interpret the rules (or the intent of the rules, I would imagine.) The rules on Attempts (as well as in other parts of the rules handbook) seem to allow for some discretion on the part of judges to make individual calls. One legal philosopher called this the difference between the "core" and the "penumbra" of a system.
I think it's fair to say that perhaps Mao should count herself lucky that she was not punished as she
could have been, as other skaters and perhaps herself have been punished before for failed attempts. However, I don't think it is clear-cut that such a punishment was
required. (Disclaimer: I'm not a judge so I can't say how strictly the rules are
supposed to be applied, and how "clear" this situation really is/should be for a judge!) I'm speaking from the perspective of a casual fan. But furthermore, in the context of a competition that is supposed to rank skaters on the quality of their performance, the theoretical consequences that you gave for making the fill-in 1T her final jumping pass and totally discounting her 2A just seems really counter to that ideal. So, according to my view that overall, her combined SP+LP was better-skated than the SP+LP of Joannie Rochette, plus given that her botched 3T-turned-into-1T situation seems to allow for some leeway (it's a little ambiguous and borderline)...I think the final decision to count Mao's 1T and the final 2A was actually fair and in keeping with the philosophy of awarding good skating. They could have thrown out the 1T as a whole, but really, she should have been given that 2A. So her placement would (and should, in my eyes) remain Silver.