Toe fungus

ok this is yucky
but my 12 yr old son has a very dark yellowish toe nail. Like almost 2/3 of the nail is darkened. Happened in the course of 2 or 3 weeks. At first I thought it was a bruise, but I don't think so now.
I took him to see a pediatrician. He says that he thinks it looks like a fungal infection. They don't treat those. He said the med is at least a 3 month course, can be costly, is not always effective and worse yet can have side effects. So they only prescribe it if it is absolutely needed, as in deforming the toe or painful. He doesn't seem to have any pain with it. (BTW my son can't speak and is mentally retarded)
SO. my question is, is there any home remedy that may work? He said topical ointments are not effective as they do not penetrate the nail enough and are not potent enough to kill something like this.
Sometimes as the nail grows out the fungus will go away on its own. Or it could last for years, being unsightly but not really hurting anything. He also assured me that the fungus is not catching to others, and would not spread to his other toes. He said fungus can occur as the result of a damaged or injured toe nail that allows the fungus to enter the nail bed.
I am not sure I buy all that?
Any ideas?