Some advice from a professional DIT and editor...
Transcoding on set does speed things up, provided that your data handler(s)/DIT(s) are always on the ball and have a firm grasp of the workflow. But it's been my experience that in student productions, this isn't always the case. Additionally, efficient transcoding requires fast hardware, and prior to the recent quad-core models, MBPs were no speed demons in that regard.
You'll see bigger productions do what you're thinking about doing, but do understand that these larger shows almost always hire professional DITs that operate purpose-built rigs (fast dual-processor Mac Pros, hardware RAID systems, etc.).
My best advice to you here would be to run speed tests on the hardware you intend to use on-set prior to shooting. Factor in how much you intend to shoot in a given day. This will give you a better idea of how feasible it actually is to transcode "on-the-fly". There's no shame in dumping/logging data during the shoot and then transcoding later, after the general chaos of film production is out of the way. There's far more pressing things to worry about on film sets, trust me.
Overall, it seems to me like you're pretty adamant about efficiency on a rather ambitious film. It's possible to achieve both, but it requires experienced crew and the right tools - and with student/low-budget productions, you often don't get the luxury of having both (or sometimes, either one). If it's a matter of meeting a deadline (like your grade), consider toning down the complexity. Good stories can be told without that.