Not taking chances = Good. Not backing up such critical data = Bad. Step one to safely maintaining your entire academic life is to have a good backup plan in place. Step one for safely transporting your entire academic life is the same. I say this as a student, and as one who has worked in the tech support office of the engineering building, and has witnessed many a student (and professor) almost literally fall to their knees in tears when we informed them that there simply was nothing we could do short of sending the drive away for very expensive recovery which may or may not work. So, I say as a fellow student, make sure that even if your machine never moves an inch, that you have a good backup solution in place, especially if the data is so critical.

Step two, in such a case as you are presenting, transporting a laptop doesn't have to be a dangerous endeavor. Firstly, ALWAYS ALWAYS ALWAYS make sure that the laptop has shut down, or at the very least the hard drive is not spinning (Hibernate, not Suspend) before loading the laptop into whatever solution you wind up with. This isn't always true, especially with the new solid state drives, but its probably still a good idea not to have your machine running while having it jostle around either way.

For me, when I start needing my laptop on campus it will be packed in a padded case which fits it like a glove. If its raining that'll get wrapped in a plastic bag, and then the whole mess will be suspended in the pannier from a bungee cord. My pannier is a DIY deal, luggage bag/backpack with wheels turned into a rack-mountable bag, with no laptop provisions, so this will all be DIY - but I'll trust it. I worry more about the screen cracking than the drive dieing - and if the screen did crack, I could still easily recover the data.