You could modify your theme's template_menu() to just not show the buttons in that theme... in the loop, check for the button's id and if it's login or register, just don't show it.
This is what some of DzinerStudio's premium themes do.
All we're really talking about is finding this line in template_menu:
foreach ($context['menu_buttons'] as $act => $button)
And adding after it:
if ($act == 'login' || $act == 'register')