It doesn't look like you can easily snake proof your nest boxes, however that would be the first choice. (1/2" or 1/4" hardware cloth all around the run); however, it might then just burrow under).
If not, if you don't kill it then it will keep coming back, the nest boxes are like a McDonalds drive-through for that snake.
Okay so honestly how many eggs could a snake eat? My concern is that we have recently seen opossum and little field mice around out building where we keep the feed which is about 50 feet from out coop. I would love to let mr snake live so he can eat the mice. I also thought that the purpose of a rooster was to kill things like small mice snakes,ect. Is there harm that could fall to the chickens or just a few eggs every once and a while
To my knowledge black racers(which is what this particular one appears to be) don't go for anything much larger than a small rabbit. But they eat a lot of small things and will clean your nest boxes out. I would get rid of it if I were in your situation.
I let a snake live for a while, figuring it was an even trade, a few eggs for him and he keeps the mice population down. Then one day I found him in my broody's nest on hatching day. He ate all the chicks - he had to die.