I think you're really over-thinking this. :) Any linking restrictions imposed on users defeats the purpose of blogging entirely. What's the difference between your users linking all over, and, say, a long-time blog that has literally years of content and thousands of posts, and links?
"Also, when some of the users don't take care of their comments, I don't want hundreds of links to random pharmaceutical companies coming from my site,"
Then get a better spam management tool. Also, I think no-follow is already on the links in the comments.
It;s alreayd been determined that Google sees the subdomain blogs as *different* sites, so what your users are linking to isn't hurting you any.
(And really - I have the opposite problem. Google LOVES my site and won't leave me alone, even when I tell it to go away.)
I think you're barking up the wrong tree here, and if you followed through, you'd be hurting yourself more in the eyes of your users, and lose some integrity to boot.
If you are bulding up a good site with loads of content and *happy users*, then Google will follow.