I'd actually think that a stern launch would be more logical. That way, the pod doesn't stand in the way of the mothership after launch, but rather allows her to hit the pedal and get out of the storm without doing any fancy maneuvers.
If the pod were something ejected at high relative speed, then perhaps bow launch would be good. But I'm fond of T'Girl
's idea of something that looks essentially like a travel pod, only with sensors in place of the window, and with a narrower docking collar - and is not as much launched as it is jettisoned (the term also used in the TOS episode), at low relative speed and without significant propulsive capacity of its own.
The bonus of this sort of thinking is that it agrees with TOS-R and makes use of all the pseudo-logic already associated with that. Such as the proximity of the shuttle maintenance facilities, the clear path for Finney to escape to Main Engineering, the idea that Finney would take quite some time to get to the location from his quarters or whatever, and so forth...