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You should be able to click into the stroke text field and type "2 pt": OmniGraffle will automatically convert from whatever units you enter to the standard units used by your canvas. (While your mouse pointer is still in that text field, you should be able to use the Up or Down arrow to change the stroke's thickness.)

If you wish to change your canvas units to something else, you can go to the Canvas Inspector, scroll down to Units (fourth section from the top), and change Units from inches to points. (Most of the new built-in templates in the Software Design folder use points or pixels by default, rather than using inches or centimeters.)