The missions are flown through that airspace multiple times per day, and it's all for national security purposes. You can't put a hold on all commercial air traffic every time, and you need to train the pilots to navigate and communicate through that particular airspace.
Whether the system (i.e. separating rotary-wing and fixed-wing traffic there) can be more safely designed is a question for the FAA. The military aircraft are simply abiding by FAA rules for that airspace. Many more civilian helicopters are doing the same thing.
If the system can’t be safely designed with a safe margin of error then it is too dangerous.
There are alternative ways and locations to train.
If there’s a nat sec issue have the planes hold.