I am going to sound mean here but this appears to be a classic case of over engineering a solution to a simple problem. I may be wrong and please feel free to correct me, but the use of a sophisticated heating tool such as a Magnetron water heater seems very over the top when for years manufacturers have been providing exactly what you are aiming to achieve using simple high efficiency micro boilers.....you have likely used one many times..... the humble electric shower

Cold water comes in at various temperatures depending upon the time of year (in UK anyway), it passes through a safety pressure monitor to ensure that the supply pressure is adequate, it then passes into a micro-boiler that can be rated at very high wattage provided over temperature and water flow monitoring is in place. 10kW heaters are common in such devices ! Temperature is controlled either by water flow through the boiler or/and thermostatic temperature control of the boiler. It would be relatively simple to design a closed loop temperature control for the heating element drive.
You may have very good reasons for wanting to use a Magnetron for heating water but please consider the KISS principle here. Magnetrons are nasty bits of kit if not handled correctly. The HT supply WILL kill you if you get across the 10kV capacitor and the RF output WILL blind you if you are exposed to its full RF energy for any length of time. I love Magnetrons as I worked on them in RADAR systems and they offer a great way to heat food in a containment situation BUT as an alternative to a nice safe and simple water heating element....nah doesn't sound a great plan .... sorry. To use Magnetrons you need to understand high Voltage safety, RF theory of Microwave energy production and RF theory of microwave transmission combined with low SWR containment. If you don't have experience with the use of microwave energy, at best you will destroy the Magnetron very quickly indeed, and at worst you will be rendered permanently blind with fried Retinas. If this is a commercial idea, it dies the moment you consider parts and maintenance costs versus a conventional boiler.
The Chinese are even selling tankless water heaters for showers !
http://www.cn-haiot.com/products/7-000W-Made-In-China-Tankless-Electric-Shower-Heater-Siver-Black-1303699.htmlCorrection...the term 'tankless' is misleading (it still contains a micro-boiler)....it just means that it is an 'on-demand' electric water heater and not a stored hot water tank system. Language differences !
just my 5 Cents and I know its not what you want to hear but sometimes you need to step back and ask yourself whether you are doing something logical and in its simplest form, or just over-engineering the solution for the fun and challenge. The latter case can make little sense in terms of the required result.