Overall, I agree with the OP. “Astonished” is not a word that seems to fit, as it implies suddenness, and one does not suddenly read a book.
That said, The Lives of a Cell by Lewis Thomas left me astonished.
Being astonished by a book in general is strange. I’m always astonished by a certain part of a book. One way I am astonished when I find myself enjoying something I wouldn’t think I would. The first example that comes to mind is actually a webcomic: Homestuck. The writing is terrible, the jokes unfunny, the dialog sounding like it comes from one person, but the plot (once it finally kicks in) is so engaging and suspenseful that I find myself checking three times a day if it’s been updated.
I was also astonished when I figured out that a lot of classical writers wrote in a way that I would consider bad. For example, Hawthorne would make asides to the reader all the time in The Scarlet Letter.
Finally, I was astonished when we got to read a book with cuss words in it in school, and even more astonished when we read that book where the kid was nearly blinded by his brother instead of looking into the sun (Can’t find it on Google). And then a bit astonished when my sister brought home The Chocolate Wars. All from this town in the middle of the Bible belt. We have more churches than do many entire cities.