get_user_meta() in multiste with respect to subdomain

You could catch and store the data separately on a per blog basis by filtering the user meta update call, via the update_user_metadata filter…

function myplugin_init() {
    add_filter( 'update_user_metadata', 'myplugin_update_points', 10, 5 );
}

function myplugin_update_points( $null, $object_id, $meta_key, $meta_value, $prev_value ) {

    if ($meta_key == 'qa_point') {

        remove_filter( 'update_user_metadata', 'myplugin_update_points', 10, 5 );            

        global $wpdb; $blog_prefix = $wpdb->get_blog_prefix();

        $current_blog_points = get_user_meta( $object_id, $blog_prefix.$meta_key, true );
        $points_change = $meta_value - $prev_value;

        if (!$current_blog_points) {$new_blog_points = $points_change;}
        else {$new_blog_points = $current_blog_points + $points_change;}           

        update_user_meta( $object_id, $blog_prefix.meta_key, $new_blog_points );

        add_filter( 'update_user_metadata', 'myplugin_update_points', 10, 5 );
    }

    // this means: go on with the normal execution in meta.php
    return null;
}

This will automatically store points for a blog via an extra user meta entry (only) when the global points are updated. Then you could have a separate function to retrieve those points for user for a blog (2nd argument optional, defaults to current):

function myplugin_get_blog_points($user_id, $blog_id=false) {

    if (!$blog_id) {$blog_id = get_current_blog_id();}

    $meta_key = 'qapoint';

    global $wpdb; $blog_prefix = $wpdb->get_blog_prefix($blog_id);

    $points = get_user_meta( $user_id, $blog_prefix.'qapoints', true ); 

    return $points;
}

Note this may not cover other functions handling points data within the theme, you’d have to check if it modified points via anything besides update_user_meta (eg. delete_user_meta) and add more code to adapt to that accordingly too. It may or may not be too difficult to be worth the hassle, but it seems possible.

Also note this will note handle points retrospectively, meaning you won’t know from which blog the points came if they already exist – that will only start to be recorded once you have code like this in place.