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First of all, I would like to say that the geek in me sympathises a lot with what you say in your comment.

With that being said, how can people who see this as a problem prevent such things? Because, and I'm extrapolating here from the comments on this thread and my personal opinion, a lot of people seem to find the prospect of running non-native Haiku applications ontop of an interesting alternative Os like Haiku pretty attractive by itself. It may not be what you or even the core developers envisioned, but since the operating system is licensed under a permissive FLOSS license, people will start to do what they always have done if they have the possibility and means to do it: They will start to tinker and come up with crazy and sometimes even scary ideas.

The problems and inconsistencies you describe are imho not specific to Linux (although the Linux family of OSes is a good subject to study these effects) but are to varying extents part of the whole software development process. If a foo does not provide means to achieve bar and if bar is even remotely related to foo and important/interesting enough for a sufficiant number of participants in the ecosystem, either foo-bar will be developed or somebody will start/port an alternative to foo. The cathedral method tends to stop working once you open the bazaar.

Short of trying to keep the "official" Haiku distro as close to the "vision" as possible and ignoring everything else that happens in this space (which would likely increase the number of distros around, if Haiku by itself is viable enough to generate interest beyond the spheres of BeOS enthusiasts) or trying to make Haiku so cumbersome to work with that nobody even thinks about developing / porting applications for it (which would be a tad counterproductive and does not always work as expected, cf. Symbian :-) ), I'm afrait that I see no way to prevent a scenario where Haiku can be used in ways not desired by the enthusiasts.