The whole issue with the nuBSG's Pegasus kamikaze attack is that we have no frame of reference for when she starts her terminal attack. The only thing in the background is the starfield, and if I remember the camera is not static, making it incredibly hard to find a frame of reference from which to measure the acceleration. The end result is that the 'sense' of acceleration is entirely left to the viewer, and may have been exaggerated by the camera movements.
Also BSG is a universe where humanity has managed to manipulate gravity. While not an 'inertial dampening system,' the Colonial Fleet has the capability to engineer a device that adjusts the internal gravity of the ship to counteract the external acceleration. We can assume this device exists because the Galactica performs many high-torque turns and everyone and everything inside is not thrown radially outward.
Also humans can withstand 9 Gs of acceleration before blacking out, and many more before actually dying.
EDIT: Just watched the entire sequence, to my eyes it appears that the Pegasus isn't accelerating all that fast, the motion relative to the camera appears nearly constant.