Most people seem to forget that CI classes are often stronger than their equivalent MTF classes, because of what I like to call the "home field advantage". A majority of the time, the cards are stacked against CI when they enter the facility. For one, they take 15-30 seconds to get through checkpoints or keycarded doors, which Foundation personnel get through instantly. Second, their spawn is basically in narnia to how far they have to walk to get back, compared to MTF/Gensec which can wait 3 minutes, then walk back out and find CI again. 3, almost all the time there are a lot more people on Security/MTF, then there are on CI.
Yes, if you look at the raw numbers on the classes themselves, they are not balanced. But there is a lot more at play than that.