Moif, where your index finger rests on the top of the holder should still be very close to the point. All pressure for shades should be applied through this finger, minimising the force necessary. To weigh in on the post in general, I don't think you necessarily need to hold the pen further up—not by much anyway. Perhaps I am unusual, but my thumb is generally only 1–3 mm away from the flange, and my grip is very light; I never experience hand fatigue.
The way I learnt this grip was by doing lots of hairline exercises (a good opportunity to study letterforms or fundamentals) with only the thumb and middle finger on the holder, index slightly raised. Before I started a stroke, I'd consciously check I was holding the pen very loosely. After something like a few days or a week, the loose, two-finger grip felt fairly natural and easy enough to control with precision. Then I started to phase in shades. Like with the lightness before, I was consciously applying all force with the index finger, and again it soon became natural. I suspect I also owe much of the lightness of my hand to this process.
NB: Most I've read in the thread so far appears to be assuming you're not going for Spencerian or OP, for which the grip should be very different.