Since the flavor seems to be that the radiation kills the crew but doesn't damage the ship.
They could be made radiation immune, or given a tag that allows them to be radioactive but not die from it (and also protects them from neuroplague).
Real Men shouldn't die from radiation....
More seriously, radiation can damage electronic gear, but it would be nice if the better autons (300D and up) automatically got radiation-proofing, regardless of what armor is fitted. There's a small bug that allows "cleaning" an auton in the constellation, but I'm about to write a ticket for that.
Edit: Done! (http://ministry.kronosaur.com/record.hexm?id=1612) (Only with slashes, which the ministry currently removes)
Makes sense to me.
Starting in 1.9 Beta 3, autons, Luminous ships, and CDM ships cannot be killed by either radiation or neuroplague.
We've defined two new properties to tag such ships:
core.noBiologicalEffects
core.noRadiationDeath
Note: In the case of radiation, the object still becomes irradiated, but never dies from it.