Hey, I like simulation. I like having a in-world explanation for things that happen in the game. I encourage my players to create such explanations, and I push myself to do the same. It's when simulation trumps fun that I start to have a problem with it.
I'd rather the in-game descriptions allowed for rapid recovery, to be honest. I don't want one guy's "realistic" injuries grinding the game down. I also don't want it so realistic that after the raid on the Caves of Chaos, everyone has to retire due to health issues.
That said, I agree wholeheartedly that dissonance occurs when a particular rules element doesn't match the overarching principle. I had that problem with more than one 3e mechanic, or mechanics in other games. I rarely let the dissonance ruin my fun, though. That's my point. I do regret that the dissonance makes it more difficult for some to enjoy the game.
I think this sort of dissonance is hard to purge from any really complex system. In this case, the complex system is the game rules and the large number of people that have input into them.