Neither bad deeds, or ommissions to do our duty, cancel out good deeds. Nor do our good deeds cancel out our bad deeds. We are all that we do, good, bad and in between.

You are of course free to regard Emma's failure to call on her neighbours more often as unpardonable. But I do not think that everyone in Regency England would have shared your view. Mr Knightley still manages to be friends with Emma, despite him being so aware of her grave faults as to hint that she should visit them more often. So Mr Knightley manages to pardon her failure to visit, even if you do not. Mrs Weston and Mr John Knightley are also the other people who see faults in Emma, and yet they still manage to be friends with her. As you mention, the Bateses also seem to feel absolutely no pain on that topic. In consequence, I do not think that JA intended her readers to regard Emma's failure to visit the Bateses as unpardonable.

You say "We would, however, I feel, be remiss if we allowed too much leeway in her faults and mistakes". I do not think that I owe any duty to think that Emma's failure to visit her neighbours is unpardonable. Quite the opposite - I have been pardoned for worse sins, it would be silly for me to adopt an unmerciful attitude towards Emma's failure to visit her neighbours. I have read _Emma_ many times in the past in a more lenient frame of mind than you recommend, and I can't see that I have come to any harm or done any harm by it.

I also do not think that anyone can be rude to someone in their thoughts. Our minds are our own spaces. If etiquette mavens take it on themselves to lay down rules for what we can and can't think, they are overstepping their bounds.

Why do you read "stocks" as referring to the Bateses' food supplies?