Marc Bruni picked the girl who got an advantage (who would spend the "quality (learning) time" with Nikki Snelson), and had no say in who got kicked off. Upon seeing the show, I thought Bruni was a real class act, and by the choice he made as to who got the advantage, any thought of a conflict of interest was removed. Very well handled.
What they did to the auditioners durjng the actual audition, on the other hand - SPOILER ALERT
Having the acting partner blow a line in an audition just didn't seem appropriate. It's one thing when you're doing a show and have rehearsed it and can jump in if someone blows a line because you know it and your acting partner well - but this didn't seem to make sense, to judge a person auditioning by how they react to a blown line. Logic tells me that if your acting partner blows a line during the audition process, you'd expect to just go back a little, and wouldn't you be on book at an audition anyway? I know they announce this is more grueling than a real audition, but this makes the audition process seem even more cruel than it really is, if that's imaginable.