Ideal Voltage/Current Sources in the Theoretical Total Resistance of a Circuit
I am assuming you are talking about a "linear" circuit.

You don't have to deactivate the internal sources.

You can "measure" (by simulation, if you're talking about a circuit that only exists hypothetically) the output current (remembering that current is taken as positive when it flows in to the port) and voltage with any two different loads connected (say two different resistors, or two different voltage sources, or two different current sources). That will give you two points on the I-V curve of the output port. Through these you can draw a line, and the slope of that line is the equivalent resistance of that port. 

If you're talking about a nonlinear circuit then you can not disable the internal sources. And you must choose two loads that do not disturb the operating point significantly. Then this method will give you the differential resistance near the operating point.