If you don't want the banner navigator in your theme you can remove the dynamic content spot that includes bannerNav.jsp. But there are two other places that must be changed at the same time.
The new theme has a model behind the scenes that holds the current user's navigation model. This model is "primed" by specific calls, instead of being loaded dynamically. The navigators play an important role in the priming so when the banner navigator is removed the priming is in complete.
1. Remove "topNavLinks" from the list of names in the navPrimingContainers parameter of the commonInit call in theme_.html because it no longer exists
2. Change the selectionPathPrimer loop in config.jsp to begin at zero (0) instead of 1 so the first node in the selection path is primed (this was previously accomplished by priming the topNavLinks)