Knowing what little I know about SEO, I love having the title within the URL.
Permalinks is set within the .httaccess file as you state. I think with the MU version of WP that we run, it's actually controlled from with WP. You may want to suggest this feature in the forums there since it would require a change with the software.
I agree with wank though. I host a little over 300 WP blogs myself, we default to the title rewrites on our install, and I've yet to have anyone change it that I know of. I had one turn it off completely but he only did it because it was interfering with a game he hosts further down in a subdirectory. Why he just didn't move it into another directory, I still don't know...
I do know I've talked about this before and it bothers me not knowing what a post is about before I click on it in the dashboard.
Honest answer, if you really don't like this feature, I think you might be happier with paid hosting and modify it yourself. I'd mention it within the MU forums first though as it may be something as simple as something being overlooked by the developers.