Something like that. You can't beat a reference capacitor for calibration, though.

Also, please see the edit of my prior post about getting the correct value for a gimmick capacitor on a PCB.

 

I still don't know what kind of accuracy you are shooting for, but I will go ahead and comment that if you can get your hands on a precision capacitor of about the same capacitance you expect, that should help you verify the calibration of your capacitance measurement method. If you are going to be using 10,000 pf or less, you can probably find some good precision NPO or COG capacitors with which to calibrate your instrument.

One thing that bothers me about your calculation is that I did not see the duty cycle of the pulse figured into it. That's important, you know ;-) While at it, the forward voltage drop in the diode will probably be very significant as may power supply variation, adding to the importance of calibration to a reference capacitor.

Edit:
I had to frequency compensate the feedback on a VHF closed loop amplifier and knew it was going to come out to about 0.5 pf but I did not want the signal to be over damped, so I had the PC designer lay out a "gimmick capacitor" -two traces side-by-side a little longer (higher capacitance) than I thought I would need. The placement of the capacitance with respect to the rest of the circuit was also very critical. When the first proto run of PCBs came in I carefully trimmed the lengths of the two parallel "plates" with an X-Acto knife until I had the waveform I wanted and informed the PCB designer of the correct length. Subsequent production runs gave entirely satisfactory results.

What is the viability of finding capacitance empirically by using a frequency generator and simply adding the capacitor to the circuit? (if you know what I mean). I discovered this method from coupling my body to audio circuits. On the scope I could see a relationship though I'm yet to work out the math.

 

At the risk of taking this thread off topic, I have an LC meter that relies on an inductor with about a 20% tolerance and a 1% capacitor and with this combination I can measure both inductors and capacitors with pretty good accuracy.

I have attached the zip file containing the C source code for that meter. You should be able to clearly see how the math works out.

If you want, you can follow up via "private" message so as to avoid dragging this thread further off topic.