The Bunkhouse became the Honors house around 2000 or so. Not sure if it's still that today. I think the issue back them had to do with the kitchen in the Bunkhouse that only the athletes could use. Could be wrong though.
As a resident, RA, and assistant Hall Director, I lived in Downey and White halls for four years total. Great experience and I wouldn't trade it for the world. Downey had just been renovated when I moved in (1997), and the plan was to renovate Orr, White and McIntyre in the few years after that. I didn't deal much with Hill or Crane hall, and they housed mostly non-traditional students back then. These renovations were mostly cosmetic, involving beds, desks, countertops, etc. None of the structure was touched then. I know there was a plan back then to completely gut one of them (McIntyre, I think), and turn the rooms into suites. The suites would sleep two or three each, and share a bathroom. the plan was nice, but I don't think the money was ever found. I'll also say that the halls were outdated during that time, but they were liveable and everyone was able to make do.
As for athletes in the halls, the policy back then was to keep several of them close together in one hall, but to spread the teams out throughout all of them. I think this actually came from the athletic dept, and was intended to get the athletes to know other students, and to hopefully attract the students to watch their friends play. It worked to an extent, and I know the Res Life people didn't mind as it kept problems from large groups of athletes to a minimum. Throughout my time, I had residents from football, basketball (mens and womens), soccer, swimming, and golf. Always at least two to four on my floor if any, and they were some of the best kids I had for the most part.
I'll never forget having to deal with a noise complaint that someone made on Patrick Chukwurah. He was just playing music loudly, and had a couple of his friends (and a couple girls) over. I knocked on the door - not knowing it was his room - and this beast of a man who could probably break me like a toothpick answered, I think looking for the pizza guy or something. I asked him to turn down the music, and he complied pretty willingly after a minute or two. Never had another complaint on the guy, and he always said hello to me after that.
IMO, separating athletes is a bad idea. They need to feel like they are part of the university culture, and the other students need to see them on a regular basis. It helps to bring that personal connection to the team, and build a culture that supports the programs.
GO POKES!