Not an expert, but if you have spent some time around medical personnel, you have pry noticed that everything in medicine is based on trends in data and this is a truth that persists in medical school admissions. One bad semester or year with subpar performance compared to consistent excellence, especially when you are hypothetically stepping into both a new social and academic scene to expand your personal horizons, will not be a nail in the coffin I imagine. A sustained trend of meh performance could be a significant detriment though. Additionally, if your timeline was to apply at the end of junior year, that pry wouldn't be a good decision considering the GPA trend once reaching upperclass coursework would be the trend by which you would be judged.
The most important things to keep in mind are these:
1) What's done is done. Keep what you learned about why your grades dropped in the back of your mind, but don't let worry deter your ability to perform well. You need to concentrate on finishing strong, and worrying about the past does absolutely nothing to move you towards the achievement of that goal.
2) GPA is an important measure, but it is only one measure by which you are judged. Regardless of where your GPA numbers fall, your MCAT will likely hold just as much weight as your GPA. Concentrate on destroying that behemoth if you haven't taken it already.
If you are talking about the West Coast USC, Fight On