Hi. I faced the same thing. I'm a total noob with WP, so take the following with that in mind please. What I did was....
I simply moved the 'wordpress' directory (including its subdirs) up one level, so that it was sitting in the domain root. I'm not certain, but I probably also edited the existing index.php so that it pointed to the correct folder (basically the reverse of the instructions on the page you linked to.)
This worked, but I found that I only had the option to have blogs in subdomains, not in sub directories. Not sure why; there was also a problem with how WP constructed the site paths, something to do with my blog being "more than 1-month old," which made them go 404 every time (I posted about this within the last few days.)
What I eneded up doing was taking a backup/export of the entries etc (in the Tools menu), and then doing a totally fresh install with an empty database. Once I did that, everything worked.