Simply, if the rule wasn't adopted, the event couldn't be ECF-graded. So you either use the rule and grade it, or don't use the rule and don't. The Laws of Chess only permit one illegal move losing, and after receiving feedback from junior organisers, it introduced the flexibility for under 11 tournaments. An event as prestigious as the Gigafinals really should be graded.
My experience of the two Gigafinals was interesting. The Southern Gigafinal was a lot bigger, as expected. My general impression was that while the top of the Southern Gigafinal is stronger, but also the bottom is weaker. The rule was in force at the Northern Gigafinal the week before, and I asked the various sector arbiters of the Northern Gigafinal how many illegal moves there were in the 12+ sections, and I don't think there were more than 2 in any one round across all the sections. The Southern Gigafinal had more than that number in raw terms, but of course it was bigger. Again, I asked about how many games were lost by illegal move, and no one mentioned the 1... Ng6 story.
I realise it's not the point, but when I asked a supplementary question at the Northern Gigafinal, the general impression that there were no "miscarriages of justice". Most of the illegal moves in the Northern Gigafinal came long after an equivalent game played between two league-chess playing adults would have been resigned by the player who was losing. I'm afraid I didn't ask the same question of those at the Southern Gigafinal - there were rather more playoffs to arrange at the end of the day.
As ever, if there is enough discontent with a rule, the best thing to do is to build support for changing it. But that process starts with lobbying FIDE.