Method Ext.app.Controller.getController() is deprecated (which was the right design decision, I think) and the documentation clearly suggests using this.getApplication().getController() instead (which is also the right thing, I believe; and it does come in handy sometimes!).
But Ext.app.Application.getController() is, indeed, marked as private now. Which, to me, contradicts with the suggestion above. Unless Sencha developers have some other plans on that part of Sencha Touch 2 architecture, I would ask to "release" Ext.app.Application.getController() to the public again (by removing the "private" tag from it).