Through SharePoint Designer, you cannot cause an update to an item to not trigger workflows that are listening for it. But, you can cause the workflow to basically be skipped with one extra Step.
Try checking out this article at Microsoft Office, which discusses secondary workflow interactions in SharePoint Designer. In the first step, it identifies whether an item was created by a specific workflow, and cancels the workflow if it isn't. We just need to adapt this - if we successfully identify the item as being modified by your secondary workflow, then we want to cut off the first workflow.
You need to create a new Step in your initial workflow, and move it to the top. In it, choose the Compare Tasks
Condition. In that condition, set field
to be "Workflow Name", leave the operation as "equals", and set value
to be the name of your secondary workflow. Then, add a Stop Workflow
Action, specifying some appropriate workflow history message to indicate that the workflow was triggered by the secondary workflow so it was terminated.