WPMU Site Wide Google Analytics vs. Local Google Analytics

I was wondering what the best practice is regarding implementing Google Analytics on a WPMU install. The solution I’m building would want to allow individual sites to have access to Google Analytics, and may be migrating their site from another implementation. I have the Google Analytics plugin installed for site-wide tracking so I can see the entire network.

However, I’m concerned about

1. Data integrity with having two analytics scripts on a single site

2. Individual clients having access to their analytics. Google Analytics only allows up to 50 users, which would not be ideal for this project.

If anyone has any advice on this I’d appreciate it.