John needs money to buy the farm he has always dreamed of. If his aunt dies this week, John will inherit the needed money from her, although John does not know that. He does not like his aunt very much. Miles away, his aunt is stuck in her home, which is in flames. Mary breaks into the house and saves the aunt, who would have died otherwise. My question is: did Mary (unknowingly) harm John? (I am a lawyer.)

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 ...
Law

Suppose you have been wrongly accused of murder. You know you are innocent but you also know that the states attorney believes you are guilty. The attorney offers you 25 years if you plead guilty but If you go to trial you will be executed if you are found guilty. You are unsure of your chances of winning the case so to prevent the possibility of death you accept the plea. Does the fact that you chose the plea bargain mean that you acknowledge that it is better to have a plea bargain than not have a plea bargain? If it is better for you to have it than not have it then does that mean that someone who would consider such a plea bargain to be coercion is wrong?

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...
Law

Sometimes, we force people to conform to the law, regardless of what they might want. Other times, we reform the law in order to more properly reflect what our citizens want as a society, how they live their lives and how. How do we decide when people should conform to the law, and when the law should conform to society?

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.