If "Resistance to Scoring" were the ONLY criterion, that is the sole and only thing on which courses were judged, then hell yes the system would be flawed, because of course difficult does not equal good. One only need play The Ranch at Silver Creek to see the proof of that.
BUT the fact is GD uses this as one out of many criteria.
So as one criterion weighted correctly with many others, heck yes it's relevant. The game is nothing without a challenge. And remember this isn't about distance, or penal nature, or any one particular WAY a course gets difficult... tricky greens could do the trick just as well.
The idea is just not to give it too much weight. It's one criteria, that's it. Many courses are not so strong in this category and are still great overall, many courses are also very strong in this category and still suck overall.
TH