WordPress MU

So, I learned that WordpressMU requires the site not have a www. at the beginning of the domain name, and strips it out if you put it in. Well, in my site, we need the www. So, I went in, and put the www. back in in the database, and WordpressMU was acting a little screwy after that. It wouldn't let me log in, except as the admin (Infinite redirects on the login page), and even as the admin, I could only edit the main blog.
So, I commented out lines 9 and 10 of wpmu-settings.php, and it started working.
The lines in question are:

if( substr( $domain, 0, 4 ) == 'www.' )
	$domain = substr( $domain, 4 );

My question is this: will this have any effect anywhere else on my blog? I haven't noticed anything so far, but if anyone knows if this will cause problems, please tell me. My site uses subdirectories for the blogs, rather than subdomains.

Also, why is this even in here? Why was the decision made to not allow WordpressMU to work on sites with a www. domain?

Been much discussed previously. I've added the 'www' tag to this thread as I see many of the previous discussions already are tagged as such. You may want to review them.

Look for a thread started by myself. It was a ridiculous decision to educate all of you how the web should work according to some and force you to comply.

I still don't see the problem?
Set up your DNS so that the www CNAME points to the main domain. Set up your webserver so that it accepts the wildcard domains and if someone puts http://www.yoursite.com or just yoursite.com, both will resolve to the same site.

Why FORCE your users to type 4 extra un-needed characters? Both www. and non-www. should resolve to the same place and in WordPress MU, they do.

Some of my users insist on advertising their sites with www. even those with subdomains (www.sub.domain.com).

My DNS handles the www and WPMU does the rest.