To be honest, I don't really know, I'm basing my argument on the fact that every decision made by uefa in the last thirty years is designed to widen the gap and maintain the status quo throughout Europe! As I mentioned, the article seems to have made little attempt to work out who benefits. It was fairly inconclusive and not particularly well argued.
Your example doesn't really address much, we could just as easily give an example that helps AFC. The point of the away goal however would have potentially stopped the dons from playing for a boring 0-0 draw away from home rather than trying to sneak a goal knowing the reward.
I'm not saying you're wrong, obviously, just that the article and subsequent examples don't really get to the heart of the issue.