Funny you should mention the secondary...I was looking at the admissions process sheet that they give student interviewers and saw that the secondary app and essays are (as you imply) used to help determine interviews. However, I do not believe that your essay put you into the reject pile. That being said, if you were already a mental midget and happened to get a 17C (I know it doesn't go that low for the essay) on the MCAT, this late in the interview cycle, well...
Oh, by the way, I have never even seen a secondary essay. Our file for interviewers does not contain the secondary.