The issue I see if you're trying to create a matched termination, is that except for the one at upper-right, your terminations are all short circuits, not matched terminations.
Since your frequency band is exactly one octave, it's possible that you could design the length of the CPW from your probe pads to the short-circuit to be approximately 1/8 wavelength, so that the short will appear as a match when seen from your probe point. This will work well for a narrow band around, say, 1.414 GHz, and will be a very bad approximation at the edges of your band at 1 and 2 GHz. If you have space, you could make different test structures with different lengths for testing in different portions of your band.
If you can work out how to do it, the option at upper-right would create a matched termination over a much broader band, but as you say it would require very careful design to ensure it's really a broadband 50 Ohm termination. From a geometry p.o.v., I'd suggest using a symmetric structure with 100 Ohm resistance from the central trace to the ground on each side.
An option that might be even better is to build a "through" structure instead of a stub structure. Put probe pads at both ends of your transmission line, and use two probes. Then let the VNA and its 2-port calibration math work out the errors due to the slight mismatch of the probe at the far end, instead of relying on your assumed-perfect 50-Ohm load as a reference for determining the trace impedance.
You can use a directional coupler to measure VSWR (reflected power). There are many app notes online for this: http://www.minicircuits.com/app/COUP7-2.pdf here is an example.
However, the fact is that waveguides need to be tuned because no two are exactly the same when you put multiple components together. This means you won't be able to just change the height a set amount to 'fix' the match. You could characterize each component and get a set of "heights" to adjust, but I would recommend trying to have a control loop where you are constantly measuring the reflected wave and tuning to minimize power.
And again, the VSWR is kind of a derived term and it will be best thought of as "tuning for minimal reflected power" when setting your system up.
And wowzers, I just saw that you have a WR340. Those are gonna be some hefty stubs!
edit: Do you really expect your match to be that dynamic? If not, you can just tune your waveguide piece on a network analyzer, epoxy/lock washer the screws and you'll have yourself a well matched piece.
Best Answer
There are many reasons that the magnetron antenna does not stick directly into the oven cavity of a microwave oven.
If it did, it would physically interfere with objects (food and dishes) inside the cavity, and it would be subject to contamination by food spatter.
The magnetron and its antenna get quite warm during operation. Having the antenna exposed where it could be touched would expose the manufacturer to liability issues because of burns. The waveguide also functions as an air duct to help cool the mangetron.
The impedance of the cavity is not a good match to the impedance of the antenna. The waveguide functions as an impedance transformer so that energy is coupled more effectively from the antenna to the cavity.
The impedance of the oven cavity varies with what is placed into it. The waveguide's impedance transformation characteristics help to reduce the variation that the magentron "sees".
The use of a waveguide gives the mechanical designer a lot more flexibility with regard to the placement of the magentron, making it possible to make the overall size of the appliance more compact.