A simpler explanation is that "DO NOT MESS WITH TIME" was the simplest piece of information that could be generated by time travel that resulted in a stable loop because Harry's precommitment to follow the experimental protocol was weak.

Simplest isn't quite as important as easiest (or most probable in terms of how reality fluid flows in a loop until it forms a stable equilibrium). The latter of course encompasses the former. In this case not only is it simple (not requiring many ontological loops) it is utterly trivial given the psychology of Harry. It only has to amplify Harry's paranoia only slightly to make him pull a reaction like that. And, in fact, given that Harry hadn't put any effort into even considering risks before doing something so extreme some reaction from him that is not the brute-forced-decryption result isn't unreasonable - so could have even happened without much consistency pressure beyond a single iteration required.

If Harry were a bit more stable and had better judgement in assessing safety he would probably have taken his time when replying and written something like "Don't be a reckless fool! Forcing black swans much?" As it happens though Harry has inherited from the author an outright dangerous way of dealing with risk - he panics, doesn't think things through and makes things worse!

In the above I am referring most significantly to the incident with transfiguration experiments. As far as I know Eliezer and Harry both believe Hermione's response was appropriate - not absolutely insane! Her reacting quickly and decisively was good but the nature of her intervention was just stupid. You don't go in there and dispel the enchantement when it is the consequences of dispelling that cause the problems. You get Harry the hell out of there, seal the room as best you can then run as fast as you can to McGonnagal. She is the one best equipped to minimize the repurcussions. At very least she would get Pompfrey on hand to heal damage before it becomes fatal and most likely would be able to detect transfigured materials and do something to prevent the worst of any damage.

Harry's response to Hermione should have been "Ok, I really appreciate the thought and I was an idiot to experiment like this... but WTF were you thinking?! If there was actually a problem with my experiment you probably would have just killed me instantly."

Likewise the appropriate response upon realising that doing things like trying to solve NP complete problems with a time turner is stupid is not to abandon all use except as a sleep enhancer. It is to implement only the simplest of protocols involving the time turner. ie. as a primitive failsafe signalling mechanism that gives a warning and (potentially) prevents certain death of his friends or worse disasters in his vicinity. This is far simpler than all the other childish things he has done with the time turner and not implementing it is outright irresponsible.