That's what seems to me to be the biggest challenge too. Going from vacuum to 1 atm at 4000 mph has got to be quite a shock. Might as well just smash the thing into a wall.
Zero to Mach 5 or 6 just seems like an instantaneous disassembly manuever, both for the craft and the centrifuge itself. Did they find a way to suppress a sonic boom at the exit point?