> If a doctor tells patients that going for a run a few times a week is a good way to increase their stamina, but most patients are too lazy or busy to do it, do you blame the method of running then?

Yes, if a medical intervention largely fails in real-world practice, whether or not it is through non-compliance, that's a strike against it as an intervention. On which is more successful in practice, even if worse in the ideal case of perfect compliance, is a better intervention.

Similarly, a development methodology which fails with real world orgs, even if the failure is due to “incorrect” implementation, is a worse methodology than one which produces better results in practice.