Don't forget to clear history in your browser!
I was all but dead with this problem until I did that.
In my case, I already had my website up and running, but I'd piled up enough errors from my attempts with plugins to restart the whole site fresh. Then I had the error message described above.
Fatal error: Call to undefined function wp_die() in / (snipped) /wp-includes/wp-db.php on line 1147
I did complete reinstalls of the database, and uninstalled everything to do with WPMU on my Godaddy deluxe hosting account. I tried fresh names for my database and for my directory. It had all worked earlier, so it should have worked. Still I got the same error.
Then I switched browsers and it worked! I moved from Firefox 3.5.5 to Safari 4.0.4 and did not get the error any longer. I suspect I should have cleared the history (cache, ect) from the browser.
I am a Noob to WP and to WPMU and to site administration. I intend to use wpmu to manage 10-20 websites for 8 consulting clients. The premise is that it will be easier than making separate platforms for each. Also that they will be empowered to make their own updates.
Am I likely to be seeing more bugs (user errors) like this one once I have the site up and running with my main plugins and themes tested?
I don't like the risk of long down times while I figure things out.
Thanks for any thoughts, and I hope my browser discovery helps.