There are some very good schools listed in that second link. If my son were committed to writing off Duke or Dartmouth just to avoid checking the hetero-male box on a questionnaire (or even just because an openly gay person was the one asking him to fill out the form), I might be questioning his decision making process.
I second these comments. Why was the kid interested in the school in the first place? Does this particular question on an application materially alter what the school has to offer? Has the kid checked up on all the folks that represent the school at "HS functions - do they all wear "too much" jewelry? Also, how much is "too much"? I glanced at the list and, for most, this one experience should not have any impact on how one views the school (larger schools will generally have a representative population - maybe a little more slanted towards middle class+). If it was one of the smaller schools (no idea if any are really small), AND the experience is reflective of the school, then someone didn't do their homework ahead of time and picked up on some arbitrary positives.
If there was in fact real interest in the school, be proactive and go visit the school or do some additional homework and I am quite certain you will find that 100% of the recruiting efforts are going towards the LGBTQ community. To allow this one experience to completely remove the school from consideration is short sighted to put it nicely. While the experience itself may have been unsettling to a 16yo high school boy, an adult should explain to him the reality of the situation. In this case, the 16yo boy should not make a determination of "comfort level" based on the one interaction. What if he visits campus and the first girl he sees in kind of plain - does he then write off the school because the girls are not pretty enough?
I hope my son reconsiders so we can at least go on a campus tour or a camp. - Missed this comment first time through. Your responsibility is to explain to your son that it is not logical to write off a school based on the single experience he had. If he wants a good fit at a quality school, you cannot allow him to make decisions based on such a minor experience (certainly minor in terms of his potential collegiate experience).