In the very first issue of the APAzine Alarums & Excursions, Mark Swanson wrote that he subscribed to a simple slogan — "D&D is too important to leave to Gary Gygax." A&E started in June 1975, the very infancy of the hobby, before even The Dragon made an appearance. Swanson was describing his differences with the way spells worked in the OD&D rules as described by Gygax, but he definitely hit on one of the points I want to explore.
For the curious, Gygax responded to Swanson in a letter published in A&E #2, and quite heartily agreed. It's important to remember that Gygax was not held in the kind of regard that he has been by latter-day followers; he was a designer who had released a game, and while other hobbyists were enthusiastic about it, they were also frequently perplexed by or in outright disapproval of the rules as originally presented in the "three little booklets". On the whole, Gygax's treatment of magic seemed to garner the most controversy. Very few contributors to A&E responded positively to the quasi-Vancian system presented in OD&D, or any of its possible permutations.
In a broader sense, I think that Gygax needs to be taken with a healthy grain of salt in the old school community. Obviously we owe the man a tremendous debt of gratitude for his design, and I think his philosophy of dungeon exploration games contains a lot of things that are worth taking to heart. But there are two caveats here. First, Gygax's interpretation is just one take — whether it's in the 1974 OD&D rules set or not. Second, he was a normal person and his interpretations changed a lot over the years, like anyone's ought to. The more imperious Gygax of the 1979 DMG and the years to follow was not exactly the same as the one who had been just another gamer a few years earlier, and when he explained his philosophy and ran games for people in his twilight years (certainly too few) they reflected a different level of maturity and perspective. In the very early days, most gamers knew little about Gygax's intent beyond the sketches presented in OD&D and Supplement I: Greyhawk.
For these reasons, I think it's important to consider Gygax's approach to gaming less as the gospel truth and more as one of several valid approaches that exist for gamers interested in the old school. While there is a definite tendency in the old school community today to stress Gygax's work and approach, I think it should be taken like any other part of D&D history — the good should be used for what it is and the bad left behind, with "good" and "bad" being what's good for your game. If Gygax happened to have a few more hits and a few less misses than most designers, all the better. But nothing Gary Gygax ever said should stand in the way of you running your game the way you best see fit. And Gary would've stood behind that statement all the way.