The fusion itself is (afaik) essentially a solved problem. The trick is extracting net energy from it, since you use a lot in generating the plasma, massive magnetic fields to keep it contained, etc.
But if you just cared about the byproducts, I think that's a much easier problem.
As far as I can tell, the production version will use LH2 instead of Liquid Helium to cool the incoming air. (after which the Helium will be burned for thrust, no need to cool it back down)
It's a similar to how most rocket engine nozzles are cooled.
You mean Hydrogen will be burned? Noble gases have hard time reacting. Except xenon with fluoride and nitrogen but you want to be away when these bonds break.
http://www.iter.org/