I am not aware of any IP laws that prohibit patching, except for circumventing copy protection (DMCA). There are plenty of laws prohibiting distributing patches, but making and using them are not commonly prohibited AFAIK.
However in the EU you aren't allowed to use information obtained through "decompilation" for the purpose development/production of a substantially similar program. Which means you cannot patch any program (exception exists for the purpose of interoperability), without risking some legal liability.
2009/24/EC Article 6 for anyone interested.
It feels that implementation of that system was quite complicated. Complicated enough that quite few people must have been involved in it.
Its quite sad that developers would implement this and all keep their mouth shut.
> Is there some kind of whistleblower law that would allow someone with knowledge to come forward?
Depends on where you live, unfortunately anywhere with 'stong' IP laws you aren't allowed to patch anything. Usually reverse engineering analysis is still fine, although if there is a contract saying you're not allowed to you could be screwed anyway.
In the train case the locks were specifically for anti-competitive purposes, and so they can whistle-blow for that; and I think in the general case you can sue for misleading dealings/false advertising/etc but not for anything specific to the software locks/traps.