It is indeed a tricky subject. One should draw a line between customs of the author/editor/period and simple mistakes, errors or careless printing, but this line is not always easy.
I am currently (proof)reading Don Quixote, using
a recent fully annotated edition, and I started with similar concerns. Fortunately, the different prefaces of this edition made the situation a bit clearer for me.
Basically it said that in that time (1600s) the author paid no attention to orthography, punctuation or whatever, that was essentially the role of the printer and editor (so "being true to the author's intent" is not really a reason here), and a fair bit of "modernization" was needed for this edition, especially in punctuation (until the 19th century or so each chapter was a single long paragraph). But many other things were not changed from older, more "authoritative" editions, such as old spellings and syntax (which would be considered incorrect today) and some hesitant, inconsistent spellings. All in all, I think the result is quite satisfactory: the text is readable by today's standards, but still has an old flavour in it.
I believe the case of Jane Austen is not quite the same, since she's a much more recent author and the language, orthography was more established, etc. But probably the same factors should be considered. One thing is fixing errors and mistakes, another thing is "modernizing" the text. I would probably try to make spelling, especially of names, consistent, though, at least in those cases when a particular form appears only once or twice.