This is just my opinion, but I think we have several things going on here, and it's possible that some people are misinterpreting what they observe.
I haven't seen the savegames of everyone who's posted here, and a lot of this is just conjecture so I might be way off, but it appears to me that:
Some people might be seeing unhappiness in cities long after the effects of whipping/drafting have gone away, and without clicking on the unhappy citizens, just assume that the whipping/drafting is the cause.
Some don't think that ill effects should apply at all to a "liberated" city. They're entitled to their opinion, but I personally disagree. There are a couple examples posted above that illustrate that cities don't just pop back to full productivity just because a few conquering heroes ride through the center of town.
Some might not be aware of the cumulative effect of whipping/drafting. For example, if I whip on one turn, the next turn I can expect to have 39 turns to go. If I now draft, I might expect this to get reset to 40. From my experiences, it doesn't seem to work that way. From what I can tell it ADDS 40 turns, for a total of 79. Now imagine if a communist metropolis was beseiged for three turns. Ill effects lasting well over 100 turns are not that hard to believe.
And finally, it seems some people are just put off by the game's choice of words, and don't like being blamed for things they didn't do.
Personally, it's the cumulative thing that bugs me the most. Sure drafting twice is worse than only doing it once, and the effect should be longer, especially to avoid exploits. But there should be some kind of diminishing returns. Like if the first causes 40 turns, the second might add 20 or 30, the third maybe 15, etc.
I also think that 40 turns is too much for one pop-rush or draft. Pop-rushing should be worse than drafting anyway. 30 turns for a pop-rush and 20 for a draft would sit better with me.
Also the effect should be lessened for a conqueror. Sure, there are still ill effects, but if you come in and rebuild the city, investing in it heavily with cash-rushes and maybe adding workers or settlers to the population, as well as improving the surrounding terrain, that should show you care about the people's welfare and should reduce (but not eliminate) the effects.
As for the wording, it could probably be improved, but it doesn't bother me, as I have a good enough imagination to overcome it. Still, to make the game into the polished gem that's expected of this series, it's probably worth the effort to come up with better phrasing.
Anyway, that IMHO would be an improvement. I'm not vain or arrogant enough to demand that Firaxis change the game to suit my personal desires, but I will say that I think it's a good idea and would be one big step towards making this already great game a true classic gem like its predecessors were.