Is there a wordpress function to cleanly delete an entry in the signups table?

You are correct about the row not having much use outside of a two day threshold where a user doesn’t activate their account.

I took a look at the codebase and can confirm there is no API function for removing a signup entry. The only code that removes a signup is the wpmu_validate_user_signup() function. It checks against current signups for the same user_login and user_email. If either of those exist, it checks to see if that user registered within the last two days. They have two days to activate their account, or that user_login or user_email becomes available to someone else.

What I would do is hook into the wp_activate_user hook to remove it immediately.

add_action( 'wpmu_activate_user', function( $user_id, $password, $meta ) {
    global $wpdb;
    // Sadly the user email isn't passed into the action
    $user = get_user_by( 'id', $user_id );
    if( $user ){
        $wpdb->delete( $wpdb->signups, array( 'user_email' => $user->user_email ) );
    }
}, 0, 3);