Yoko seems more of an anti-hero than a villain, which is why Kurama and Hiei seem to get along. They get that sometimes someone has to freaking die. So if Botan does not approve of Yoko and what he does, when it's usually in self-defense these days, she is going to recognize a true monster--worse than Toguro, who could kill his own lover without a fuck given. Botan is going to think Yoko is a SAINT!

I think it was for one job where he needed a distraction large enough to alert the entire complex. So Yoko got what he needed, but the guy went above and beyond for 'distraction' and massacred them all, and I guess if we need rape as a plot device, was in the middle of raping some of the guards or whatever.