well,It is not that hard.If you are using buddypress and a user is at yoursite.com/wp-login.php ,he may see a link of registration(obviously only if you have enabled it ) which points to yoursite.com/wp-login.php?action=register.

Now if you are using buddypress compatible themes, you must be interested in sending the user to yoursite.com/register in case they click on the registration link.

Well,so here is a small snippet of code to assist you.

/*let us keep an eye on the site_url*/
add_filter("site_url","my_custom_register_url",10,3);
function my_custom_register_url($url, $path, $orig_scheme)
{    /*if the site url is used in login contentxt,let us check for the register link*/
if($orig_scheme=="login")
{
if($path=="wp-login.php?action=register")//so it is a registration link..cool
return get_option('siteurl')."/".BP_REGISTER_SLUG;//let us replace it with  our buddypress registration page url
}

return $url;

}

?>

Drop this into the functions.php of your active theme and go and check ,any reference to yoursite.com/wp-login.php?action=register  will be pointing to yoursite.com/register(or what ever you set as registration page slug)

Hope it helps.Now I would love to hear ,how it went with you or what approach you are using .Go ahead and put your views in comments.