The newly contemplated notes would have replaced the already dissonant dominant chord that's crossed out. That chord (B-D#-F#-A-C), which treats the previous FM7 chord as a Neapolitan 6th, adds a minor ninth to the B7 harmony that eventually settles into E Minor - but Beethoven considered something much more radical: an Eb7 chord over an Fb Major chord. Perhaps this was to highlight the tension between the primary key of E-flat Major and the new theme in the distant key of E (Fb) Minor. Further sketches suggest that this chord was intended to continue through the next couple of pages. Here's what it might have sounded like, with the new "harmony" showing up first at 0:10. [Thanks to René Köhler and the National Philharmonic Symphony Orchestra.]
What makes this all the more astonishing is that this "crazy" chord is exactly what Igor Stravinsky ended up using to shock Paris about 100 years later in his "The Rite of Spring."
Above, you can see the chord Beethoven eventually settled on next to the chord that Stravinsky used - and that Beethoven first conceived! So, Beethoven ended up keeping that E-flat on top (respelled as D-sharp), but apparently even he wasn't ready to unleash such a primitive sonority on the world.
More to come... [UPDATE: It's here.]