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Right, I think the busted serialization format is probably the result of a BuildReference being cleared and a different AbstractBuild being created than the FingerprintAction was originally produced with. So there are two problems:
For the second part, your proposed patch is unacceptable (I think) because it breaks the general RunAction contract. I am working on a different patch that acknowledges that the FingerprintAction is incomplete and just limits the damage (no exceptions printed, most things with the fingerprints work).
Not sure what to do about the first part. Seems like a fundamental flaw. (Though I am unable to reproduce it even by making AbstractLazyLoadRunMap.unwrap usually return null.) The best I can think of is to cache all the RunAction instances in a build using strong references so it is guaranteed they will not be collected.