I think you all greatly misinterpret the SM/USUM Pokedex entries for Mega Evolutions.
Really, it's not that simple. What they say is not meant to antagonize Mega Evolution, and it does not mean that we are simply hurting our Pokemon every time we make them Mega Evolve, or forcefully putting them in pain all the time. Rather, they are an explanation for many of the intrinsic things about Mega Evolution. Specifically, why Mega Evolution cannot occur naturally in the wild, and why it's not a permanent form of evolution.
Mega Evolutions are essentially evolved form of the Pokemon they derive from. However, the energy of Mega Evolution is immensely powerful. A Pokemon in its wild, natural state cannot possibly handle that level of energy on its own. A Mega Evolved Pokemon harnesses immense power, but that power would eventually get the better of them, and they would be unable to take control of such energy and as such would go berserk. That is why we almost never see Mega Evolution occurring naturally in the wild, and why we only see them under the ownership of Trainers. A Mega Stone under the hands of a Trainer essentially facilitates Mega Evolution, as a Pokemon under the ownership of a Trainer would be able to Mega Evolve as a Trainer would be able to channel the energy of Mega Evolution through them and their Mega Stone.
But there is a catch: as said in X and Y, it takes a strong bond of trust between Trainer and Pokemon to fully control the power of Mega Evolution. If a Trainer and their Pokemon share a strong bond and are fully in sync, that connection of trust can essentially "tame" the power of Mega Evolution: as they are in sync, Trainer and Pokemon together can take control of the immense power that Mega Evolution provides, and utilize it to their full advantage, representing their strong connection by bringing out the Pokemon's full power. However, if the Trainer and Pokemon do not bear a strong enough bond, then they will not be able to take full control of Mega Evolution, and the Pokemon could lose control and go berserk. And while I do not like using the anime as reference, we see this somewhat with Korrina's Lucario there. When she first Mega Evolved her Lucario, it would eventually lose control and go berserk. If the Trainer is inexperienced, then there is a very good chance that the Mega Evolved Pokemon would turn on them and be unable to control their power. That is why we see it harnessed largely by more experienced Trainers who have successfully achieved a strong bond with their Pokemon: they have a strong enough trust between them and their Pokemon that they can fully master and control the power that Mega Evolution provides, and utilize it to their full advantage in battles. When that happens, a Pokemon will be able to channel the strength of its bond and overcome the energy of Mega Evolution, making it less painful for them to bear and be able to utilize their newfound power and take complete control over it.
But it will eventually prove exhausting, even with that in mind. Because there is so much energy channeling through a Pokemon when in a Mega Evolved state, it will eventually give in. As such, Mega Evolved Pokemon can only remain in their evolved form for so long: once they have fulfilled their purpose in battle, they will return to their original form, so as to minimize their chances of suffering from the energy. And a Trainer can only ever Mega Evolve one Pokemon per battle they participate in: they simply cannot channel enough Mega Evolution energy through their Key stone to do so to all of their Pokemon. As such, because the energy is so immensely powerful that even a Pokemon alone wouldn't be able to handle it, there are many limitations to how it can be utilized.
Using Mega Evolution is a great power. But with great power comes great responsibility. It takes a strong bond of trust to tame the power of Mega Evolution, and unless you have a strong trust, you will not be able to use it effectively. And a Pokemon in its most wild, natural form would be unable to control such an immense power, so it takes a strong Trainer who can truly trust their Pokemon to be able to help them overcome that power and take control of it. But if you achieve that strong bond, then you have a great power in your hands, and your Pokemon will be able to use that power very effectively.
That's my interpretation of it: I probably sound weird and stupid the way I wrote all this but that's my take on Mega Evolution and summing everything up from what we've been told of it, especially with the USUM/SM dex entries.
