How to disable Drupal's module update check for CiviCRM?
There are a few options:


CiviCRM could use Drupal's infrastructure to ship CiviCRM downloads. Current CiviCRM / Drupal development process prevents this, and that's a much bigger topic and best discussed outside of this SO question!
CiviCRM could somehow suppress the update notifications from the Drupal update status page. This would hide the warning, but arguably be a worse outcome. I don't think this would deliver what you want.
CiviCRM could supply a project feed to match the existing Drupal.org infrastructure, so that Drupal can check that alternate feed URL for updates.


IMO the last option is the best balance of outcomes - it could provide accurate update notifications to Drupal-oriented administrators who might not see the in-app warnings in CiviCRM. There's a JIRA proposing this over at CRM-15769.