The problem isn’t that he can’t have children, the problem is that he is unable to have intercourse. The Church teaches that intercourse, or the ability of a couple to join together and become one flesh, is a very important part of marriage. A couple has to be open to the possibility of life, but sometimes the couple is unable to concieve. It’s impossible for this couple to have intercourse. That is why the Church will not marry them.
Thanks for the clear, succinct explanation.