Speaking from experience, I had the same scenario and have had no real problems. I "failed" the standard Ishihara screening test and they followed up with simple cards for which I had to identify the colors. I've never had any real-world problems due to my "color blindness" and this test was really, really easy. They informed my program director and we discussed that it hasn't ever been a functional problem for me. And indeed it hasn't been a problem in training (currently a PGY-4) at all. As long as he is able to distinguish colors in the real world, it shouldn't be a huge issue. Though it might be worth bringing it up to the program director ahead of time, so it isn't a last minute, stressful thing the week before starting residency.