Ah hang on, I was under the impression that users could run arbitrary crap on their local phone, just not distribute it. It turns out this is not so unless you jailbreak it and thus void your warranty or pay for a developer's license to permit "testing".
The download thing can still be got around though -- there's nothing to stop Apple retrieving the download by way of the publisher but checksumming the download as it goes through (or modifying the app store client to check that the checksum matches one handed down by the Store servers) in order to ensure that the right thing is being distributed.
Now then what about what seems to be the core problem: is it ever possible to honour free licenses on a locked-down platform? What if Apple offered an Android-style "authorised" jailbreak, in which the phone permits you to download software but breaks your warranty for doing so? Is Apple imposing illegal conditions in that way? If so, doesn't the Android similarly prevent you from replacing core system components without such a jailbreak and so break the license attached to the kernel?
Unfortunately I'd guess that Apple don't want the support headache from people who followed a HOWTO online and have screwed up their phone, their policy generally being to save people from their own ineptitude...