Is there a way to run the Organizer without XCODE to add a device to a Porthole?
Probably not since it's built into XCode and is not listed in the Developer Tools menu.
But you can open organizer without opening an entire XCode project. Just open XCode and click SHIFT + CMD + 2 or Window > Organizer.
OR you can go to developer.apple.com > Provisioning Portal > Devices and add a device manually