Having thought about this off and on for a couple of days, I think I'm going to argue mostly in defense of JKR here. The only place I'm not sure I agree with her choice is at the very existence of the Time Turner itself -- I'm not sure it was necessary to the plot of PoA. I think it would have been possible to have everything turn out the way she wanted it to without using a Time Turner. This leads me to believe that the Time Turner will prove important in either Book 6 or 7.
For the actual use and ramifications of the Time Turner -- Actually, I think she got it right. If I understand the rule correctly:
Persons using the Time Turner must not be observed using it.
Dumbledore alludes to this. "You must not be seen." I'm inclined to believe that this is attached to an even more stringent condition:
Persons using the Time Turner cannot change any event that was actually observed.
I freely admit that this is being pulled from thin air, but I believe it makes sense. There is a notion in certain fields of science that certain outcomes are not actually certain until they are observed. So once an event has been observed to be one way, it cannot be any other way. At any rate, taken together, these statements lead to a logical consequence:
Persons using the Time Turner can only use it to make things happen the way they have already been observed to happen, **up to the time at which they started using the Time Turner**.
Note that this does allow some wiggle room:
Events which were not observed, and do not change any events that were observed **prior to the use of the Time Turner**, CAN be changed.
There were two events that the trio wished to prevent: the execution of Buckbeak and the dementors kissing Black. At the time when they started using the Time Turner, the execution of Buckbeak was never confirmed to be observed. The trio heard what they thought was his execution, but what they actually heard was what eventually happened: the thud of the axe as it was thrown down by Macnair, and Hagrid's rambling. The implication is that they changed events to be the way they were observed (by Macnair and Hagrid) to be; we just don't find out until later. As for the dementors kissing Black, note that this had not yet happened. What had been observed up to that point was Black being put in Flitwick's office. No one had gone back and observed that he was still in there at the time at which the trio started to use the Time Turner. Therefore, I believe that the trio fulfilled the conditions of using the Time Turner as reasoned above. Further, I think it's possible that Dumbledore had already observed events to be other than how the trio perceived them up to that point, and already knew that the trio had to use the Time Turner in order for those events to happen properly.
On related subjects:
Nightcrawler wrote:Why can't they use the timepeice thingy to save Sirius twice? Why can't the go back and kill Tom Riddle as a pimply faced teenager? Or kill Wormtail and baby Voldermort in the graveyard scene of GoF? Or even use it in trials to prove who is innocent and who is guilty?
Because all of these events would be contrary to what has been observed to happen.
...No, instead they give it to a little girl so that she can pick up a few extra classes.
They give it to the one girl who has demonstrated up to that point that she is probably responsible enough to use it properly, knowing full well that current events are precarious enough that she may eventually have to use it for something far more important than picking up a few extra classes.
What is the difference between rushing back to the past and saving Sirius from the dementors kiss at the last moment, OR, waiting five minutes, then going back and saving the now, souless guy. Either way, Sirius would be saved from a fate that would otherwise leave him souless, so the end result would be the same. It wouldn't really matter.
Again, the difference is in the former situation, no one has yet observed Sirius being kissed, but in the latter, someone has. It is the presence or absence of an observer that determines whether or not something can be changed.
As for the butterfly effect -- I think that this particular ramification of changing events is still present, but in a slightly different form. You have to be very careful when changing things in the past, because not only can what you changed not be observed, it can not lead to changes in already observed events either. You can only change things in the past that do not change anyone's past. The future is still up for grabs, though.
Okay... I hope that all made sense. If I've screwed something up let me know and I'll try to clarify.