Why is it wrong to connect an oscilloscope in parallel with a circuit element?
If you want to measure the voltage across a circuit element which has no direct connection to ground, then the method you describe is required.  Otherwise, the ground clip on the oscilloscope, which is connected to ground, will create a short circuit in your device. The short circuit will interrupt the proper operation of your circuit, thus you will not be measuring what you want.  At worst, the short circuit could cause damage to one or more elements in your circuit.  Many dual-trace oscilloscopes can be set up to perform the subtraction automatically by means of connecting the channel 1 probe to one side of your circuit element and the channel 2 probe to the other side.  Select the inverting function for channel 2 and the channel 1 minus channel 2 function so that the oscilloscope then displays the difference between the voltages of the two probes.  This difference is the voltage across your circuit element.  There are limitations on the performance of this mode but it relatively easy to do.  An actual differential amplifier is needed to get more accurate results.