This situation should have been foreseen, and plans for Hürjet aircraft, at least in a 2 x TF-10000 configuration, should have been prepared.
By the time the time the F-35 issue became apparent, they had already decided on a single engine configuration and double engine for the KAAN. They would have had to throw out the whole design and design something like the M-346 or Yak-130, that redesign would take a couple years extra time, but even then you have engine issues, b/c even till this day, there is no TF10000 ready. Which means they would have had to get an engine off the market, and the only ones producing the engine in this class are the US with the F125 and Ukraine with the AL-322, with the F125, its the same potential issue with the F404, and with the AL-322, you are using a Non NATO soviet esque powerplant, but even that, we don't know that the Ukraine war is coming up in 2022. And again we have a risk to engine supply down the road.
So really there is no fool proof option that doesn't carry a risk.
Add to that the M-346 style trainer is not as good as a single engine F404 style fighter, one large engine fighter is usually more efficient than two weaker engined fighter, single engine fighter design is also more adaptable, and can be ported into a Lead in/Light Fighter with a stronger engine like the F414, this option is not available with a Al-322 fighter, if you get the engine at all, given that we eventually had the Ukraine Russia war.
Yes, IMO, USA will punish Germany. Because this move would lead to both significant commercial and strategic losses for the USA.
But by that logic, it should affect germans in other places, why allow them to build the Tornado? force them to buy F-16, why allow Eurofighter in the first place, why allow A-400, force a C-130 or C-17 sale. Why allow airbus to be formed, force them to buy Boeing.
I don't think a single engine variant of the EJ200 would force any retaliation, its not even a german only project, as 4 different countries are involved in the production, and and backlash would target them all.
Its just that none of them had a need for it. They did end up developing a Single engine prototype with Thrust vectoring for the HAL Tejas and tried to pitch it to India, but India went with the F404 and F414 respectively, especially after the US agreed to tech transfer for local production of the F414 in India.