Conga Orchestrate gives you the ability to disable custom object triggers created through the setup wizard with the following steps.

• Adding a checkbox field to the Conga Orchestrate Settings custom setting called "Disable_{Namespace}_{Object_Name}_Trigger" allows custom object triggers to be disabled like standard object triggers.

  Note: A single underscore between the namespace and the object name is important if there is a namespace. The case does not matter.
• When the checkbox is selected, the trigger is disabled and will not run.