Yes, with gravity-assist slingshots, parts of a very long craf could be a subject to torque due to gravity gradient along the craft's truss, and if it's not constructed to withstand these forces, it could tear it apart or deform by tidal forces. Due to this torque, the craft could also enter into a violent spin. We can actually observe similar happening to larger comets and asteroids as they shoot past massive celestial bodies, perhaps most famous of those is the comet Shoemaker–Levy 9 that that broke apart and collided with Jupiter in July 1994:
Image of Comet Shoemaker–Levy 9 fragments (total: 21), taken on May 17, 1994 (Source: Wikipedia on Comet Shoemaker–Levy 9)
Same could of course happen also during aerobraking, but mostly due to difference in decelerating forces along the craft's body due to atmospheric drag. At velocities involved, atmosphere actually behaves as a fluid, and the flow shapes along the ram-facing side and bends around its corners. As it does that, it has to increase its velocity relative to the rest of the medium the craft is surrounded with, and increases its kinetic force with it. As these deflected jets catch up with the slower flow around the craft, rapid deceleration and change in vector cause shockwaves and form local eddies along the edge of the craft's ram-facing side. This is actually easier to demonstrate than using some comets that impacted Jupiter, just take a sheet of paper, hold it above your head and release. You'll notice it'll slightly bend at its edges due to these air currents forming along its bottom side.
Oh, and using airbags as Inflatable Aerodynamic Decelerators (IAD) isn't science fiction. For example, NASA is developing HIAD (Hypersonic Inflatable Aerodynamic Decelerator), and there are other companies taking similar approach to aerobraking, for example ILC Dover developing many IAD variants. Here's NASA video of Inflatable Re-entry Vehicle Experiment 3 (IRVE-3) flight demonstration of inflatable technology, and this is how IRVE-3 looked like:
NASA's Inflatable Re-entry Vehicle Experiment 3 (IRVE-3) completely inflated under vacuum conditions in Transonic Dynamics
Tunnel at Langley Research Center. Image credit: NASA Langley / Kathy Barnstorff