LFReD, I feel your pain.
Personally, I write really, really ugly code. And when I decided to create a blogging community for military families who had lost someone in combat, all the research I could do suggested that WPMU was the way to go - this after six months spent trying Joomla, Drupal, b2evo and a pile of other solutions. Since I'm paying for everything out of my own pocket and running the site free of advertising, FOSS was a necessity.
Luckily, I had a great database of 4515 KIA's from the Department of Defense to work with, so it should have been pretty easy to do what I was thinking of.
Then I read the posts in this forum, and realized that it would be easier to create all 4515 blogs and users manually, than it would to let the "helpful" people on this forum pass judgment on what kind of person I am, or tell me that I'm an idiot for not using the search functions when it takes just about as much typing to provide a link, and maybe a minute more than that to provide actual useful information. (Have a look - you'll see that some say 'search for it yourself' more than they give real answers.)
To your question, the only workaround I came up with was to hack the wpmu-blogs.php file to auto-fill the fields in the blog create form with the values I would want for each new blog, and loop through it, loading the next blog and user to be created when the page reloads. So at least for the last half of my database, I was able to go through by only hitting "Add Blog" 2000 times - and I wish I were exaggerating.