I needed to remove the My Alfresco part in Alfresco Navigator. This is a piece of JSF hack that I'll share here. The way it is done here isn't the way it should be done in order to properly package it... but it's a hack.

Copy the source code of the org.alfresco.web.ui.repo.component.UINavigator class and remove the following blocks:

    treePanel = false;
    areaTitle = Application.getMessage(context, NavigationBean.MSG_MYALFRESCO);


if (NavigationBean.LOCATION_MYALFRESCO.equals(area) == false)
    encodeSidebarButton(context, out, sideBarStyle,

Compile the Java class and put the result into a JAR file. Then place the jar file into the WEB-INF/lib folder and restart Alfresco.

Of course you should also remove the tag corresponding to My Alfresco in the jsp/parts/titlebar.jsp page to remove the link from the page.