At the moment, the only way to modify the GUI, including what tabs are visible, is to modify the code directly.
One easy way to remove one specific tab is to edit one of two files: company_website.php or project_website.php. Both of them are located in /application/helpers/.
Edit company_website.php if you want to edit your dashboard pages (My Tasks, My projects) and project_website.php for the projects pages.
Most likely it will be the latter, but both modifications are similar.
Look for the function project_tabbed_navigation() (or dashboard_tabbed_navigation()). You'll see that it contains a series of calls to the function add_tabbed_navigation_item(). You'll understand that you just need to delete or comment out the lines that corresponds to the tab you want to see gone.
If you want to order the tabs differently, just switch one group of line for another.
Note that this method only stop the display of the tab in the GUI, it doesn't shut down the associated functions. For example, if you remove the "Messages" tab, you will still be able to add a message to a milestone for example... The links to add a message will still be present unless you make other changes.