Great question! I suggest that Mary did not (unknowingly) harm John, given the case as described. One reason for thinking this is not a harm is a kind of slippery slope line of reasoning. If John is harmed by the rescue of his aunt, many, many people are being harmed right now when their benefactors are enabled to live. You have singled out John as facing a timely opportunity (without the money this week, the farm of his dreams slips through his fingers), but I suspect that my nephews and nieces would really like their inheritance from me right now for all kinds of reasons and, while I hope they actually love me and would prefer I lived a while longer, I think it would be (at least) odd for them to believe they were harmed when I narrowly escaped death from a drunk driver car accident. Actually, come to think of it, I can imagine my nephew and niece thinking "if only that bloke had driven a little faster, we would have the funds we want from Uncle Charles's estate' so maybe this is not so odd. But ...

Great question! I suggest that if you do take the plea bargain and you think that your action was prudent and permissible (under the circumstances), then you are implicitly committed to think that others who are in a similar situation would also be prudent and doing something permissible if they did the same. But your taking the bargain is compatible with you thinking that the choice you were given (either take a bargain which involves you taking responsibility for a crime you did not commit or face execution) was itself the result of a grave, profound wrong. In your description of the case you do not stipulate whether the attorney's belief in your guilt is reasonable (there is some evidence you did the crime and, while it is false that you are the murderer most reasonable people would believe you are the killer based on the evidence). If the attorney truly and reasonably thinks you are guilty, the choice he gives you is tragic and wrong but it was based on (let us imagine) the attorney's best...

Philosophers sometimes use the terms "perfect duty" to refer to duties that persons have which they can be compelled to obey, as distinct from imperfect duties which cannot compel obedience (these duties might range from a duty to be nice / not rude to acts of amazing courage which we regard as 'above and beyond the call of duty). Some duties seem obviously perfect duties like the duty not to commit homicide or rape or steal and so on, otherwise one would not have a society. Other duties seem to be imperfect, though highly important for democracy such as the duty to vote. I believe that citizens in a democracy who can vote (they are of age and of sound mind) should vote, but evidently this is not something that the USA and other democracies believe they can force citizens to do. You might check out Joel Feinberg's excellent book Rights, Justice, and the Bounds of Liberty.