I have been dealing with Marek's for the past three years and just two days ago put down a sweet rooster who was slowly declining from the disease and refusing to leave a nesting box.
First off I am so sorry you are going through this. I have lost over 2/3rds of my original flock to this disease and currently have 11 birds remaining out of a flock of 38. So I am no stranger to what you are going through.
I cry with every one that I put down and trust me, there is no easy method. I have read about the ether method but have no idea how much you have to use for a standard sized hen. I've always employed a proper calibre bullet to the back of the head just behind the comb. They die instantly. Yes, there is some flapping around. But I am careful to use the right calibre to get the job done. For the rooster I mentioned, I used a 38 as he was a big boy. Yes, the flapping bothers me. I usually sit with the bird, cuddle them for awhile, talk to them, tell them how much I love them and how I don't want them to suffer any longer. Many just lay on the ground where I put them but some want to stand and as I want the one shot to count, I will lay those birds down on the ground, on their breast bones with their feet behind them so I can hold the feet and be a safe distance from their heads. They are not afraid. They have no idea what is happening to them. I make sure to fire a point blank shot It's over in an instant. I just make it my policy to immediately turn away and walk around for a minute, not going back until I am sure all the movement is over. It doesn't take long.
Whatever method you choose make it the easiest one for you to endure because sadly, this will not be your last loss.
As for the question about breeding. No. I do not allow any of my large birds to set eggs nor do I allow any to hatch from these birds. I am hoping to get 6 Marek's resistant Egyptian Fayoumi's next month and these birds will be crossed with my bantam barnyard mixes that have proven to be resistant to the disease in order to further their resistance.
I am so sorry. My soul cries for what you are going through

The only way to truly understand is if you are fighting this disease in your own flock and frankly, I wouldn't wish that on any chicken lover.