Adding checks against ISO loaders isn't that much of a bad idea, it'd be nice to have Sony change it's view on the homebrew scene, as right now a custom firmware comes conjoined with a large sum of ISO-related features, it's just hard to look away from them. Sure, it'd restrict the freedom, but besides, if someone can't even disable a few simple checks in the HEN code, then they shouldn't be writing an ISO loader, as they probably just stole the code off older sources in that case.
Personally I have to agree with those saying that adding more security to an exploit to circumvent security may not be hypocritical but it definitely is borderline absurd. Not coding in ISO Loader support or checking it against ISO Loading? Fine, its not on his docket so he shouldnt worry about it if he doesnt want to. But purposely working against future developers who might want to add the feature because of either a morality stance or anger at people is not in the spirit of open computing in my opinion.