Validation at node_presave in drupal 6 I received a somewhat complicated Drupal 6 application to maintain and unfortunately I am quite a newbie with Drupal.

The task is to verify certain system variable is set before saving the node. Is the node_presave ok place to do this? And how can I abort the saving process?

It should fail silently with a log message.
No, hook_nodeapi op=presave is the wrong place for that.

You should instead use hook_nodeapi op=validate


  "validate": The user has just finished editing the node and is trying
  to preview or submit it. This hook can be used to check the node data.
  Errors should be set with form_set_error().


https://api.drupal.org/api/drupal/developer%21hooks%21core.php/function/hook_nodeapi/6

However, it won't fail silently, instead showing an error on the node form.