My friends in medicine have also been working out their plans for these short days. Whether or not you will work on shabbat as a medical student is a personal halachik question and I am not here to make that decision for you. It is best done by contacting your local halachik authority. Several of my friends and colleagues have come to the conclusion that they will not. The ones at Albert einstein have no problem. The ones elsewhere have found this a stickier issue. Most have decided to contact the directors of the rotations that they are currently on. For the most part these directors are helpful and willing to work with them. Occasionally there is one that isn't, however I have yet to hear of someone being penalized for not working on shabbat in my institution. There has just been some frowning upon it. But if you are firm in your convictions you can withstand the pressure. In addition even when the clerkship director is unhelpful the residents are usually nice and will work something out for you. You may have to sacrifice all your sundays, but its worth it.
These early days are not easy. One of the best things to do is ask senior students how the different clerkships handled their requests so you can schedule yours accordingly. It can be tough to hold firm when someone is telling you "your education will suffer" if you skip a Friday afternoon session but remember your priorities and hold firm! Do not get into ridiculous negotiations. Present your situation with clarity and respect, you might just be surprised to see that respect returned to you.