That passage you have quoted about Harriet's background is what has always bothered me. As you say rightly, it was Emma's fantasy that Harriet was a gentleman's daughter, but I don't entirely like her reaction to finding out the truth. Harriet is not to blame for Emma's delusions and is the same person she always was. Emma's reaction to the truth is, IMO, too like her old snobbishness. Why is she so much less charitable than Mr Knightley? He never had any delusions about Harriet's status, but was still prepared to admit at the Crown Ball that Harriet would have made a better wife for Mr Elton than the one he chose. Emma apparently feels, without qualification, that Harriet would have been a bad connection even for Mr Elton. And then we get "The stain of illegitimacy, unbleached by nobility or wealth, would have been a stain indeed". Well, that was the prevailing attitude of the time, but Emma has got a lot less liberal-minded than she was in Chapter 8, when she said "As to the circumstances of her [Harriet's] birth, though in a legal sense she may be called Nobody, it will not hold in common sense. She is not to pay for the offence of others, by being held below the level of those with whom she is brought up". Of course she was still asserting that Harriet must be a gentleman's daughter back then.

I am quite sure that she will not drop Harriet entirely, and certainly there are good practical reasons (some of which you have cited) why their friendship cannot be maintained at the same level and must cool, but I have faint concerns lest it ends up with Mrs Knightley calling on Mrs Martin at Abbey Mill Farm and having the carriage return for her in 15 minutes.

I am however comforted by the thoughts that Emma did rejoice wholeheartedly once convinced that Harriet was indeed engaged, and she did receive Mr Martin and acknowledge his good qualities - as well she might, since he has in a sense rescued her from the perpetual guilt she would have felt - deservedly - if Harriet had remained single. And that she apparently acted as Harriet's bridesmaid - the first and last time she would give precedence to her.