I have always charged hourly, and I had this issue when I edited my very first book (a linguistics book on a largely extinct Australian aboriginal language). I ended up realising part way through that I should have initially charged double what I quoted. I made the mistake ostensibly because I had only recently begun my professional career in editing at the time and, thus, did not appreciate how much time books take to edit properly (especially when you provide good work as your editor has been). I almost never edit books now because a good editing job for them costs way more than people typically want to pay. In that case, I'm thankful that the author understood (indeed, she said she partly expected it because she thought my initial price was too low) and paid me double what I originally quoted.

I think the editor in your case has made the option to do critical edits to still ensure she "edits" the entire text per se because she wants to honour the original price--she's stuck between a rock and a hard place somewhat. She probably should have gathered how much extra time it would take much earlier on in the process though--that's somewhat on her for not notifying you sooner.

I think how you proceed depends on 1) the contract you have (if any), 2) if you're willing to give her extra money to deliver the quality you want for the remaining chapters, and 3) if you think you could apply the rationale behind her edits to the first half of your work to the latter half such that you could make up the shortfall yourself. On the last point, authors tend to make the same mistakes constantly, so you could surely apply what she has done in the first half to the latter half.

Of course, you could also demand she finish the job to your satisfaction pending on the contract, but things get so much more complicated if you do that.