The only real moral and ethical issues I see with this particular technological development have to do with the amount of money it cost. This is not really about scientific ethics, but the LHC cost huge amounts of money and will not really do anything of practical value. It seems like a real waste at this point.
I am discounting the worries that some people had about the LHC creating a black hole that would swallow the Earth. However, I suppose you could cite that as an issue. If there were any plausible concerns about that, then that would have been an issue -- whether to risk that in the name of knowledge.
The LHC is designed to accelerate atoms to hyperspeeds and collide them together, on the theory that this breaks them apart into subatomic particles. It is hoped this will open the door to greater understanding of the nature of matter and the origins of the universe.
The problem is, just as with the atomic bomb, we aren't sure exactly what will happen. That is, we are advancing technology we don't fully understand. There have been some who say such a collider could open tiny black holes that swallow all the Earth, although true scientists don't believe this and it is more of a conspiracy theory. The ethical issue is how aggressively we should pursue this new technology if there is actually any danger of results that are harmful to humans. What if this technology, as with the atom bomb, can be used as or developed into a weapon?
This facililty also has a very large dollar cost attached to it, and one can argue that the potential scientific value of such research is not worth denying that kind of funding to other areas of human need, or other research that might be more valuable to advancing human interests.
The Large Hadron Collider raises serious moral and ethical issues. Should an organization and governments sponsor theoretical physics experiments in a time of uncertainty when many people are homeless, poor, and malnourished? Should anyone fund this project while there are people starving throughout the world? This is something that can not be easily reconciled. While these issues are debated, there is no easy answer, which lends itself to more serious discussion. Should only things that have quantifiable results be attempted, or does it benefit humanity that theoretical experiments continue and one day hope to accomplish something? I personally feel substantial results will never be obtained with it.