Try cd into webapp/install/cli/ and run php upgrade.php --with-new-sql
Your mileage may vary with that though. It didn't work for me, just threw a different error, so I wound up looking at webapp/install/sql/build-db_mysql-upcoming-release.sql and running the SQL manually in phpMyAdmin to create the necessary tables/columns etc as the app throws errors, which (eventually!) seems to work fine. Switch on debug in the config so you can see what's happening.
I'm guessing you might also have some luck if you rename that last file to build-db_mysql.sql (replacing the other one) and start the installation from scratch? I haven't checked the code to see if it actually uses that script on install, but it would make sense.
Hope that helps!