In the games (and presumably the Pokemon Special manga), the Pokemon are rather less sentient, and quite happily eat each other.
In the anime…not so much. One has to either not consider that aspect, or else assume there are regular type animals hanging around somewhere, or everyone’s vegetarian. (With a handful of exceptions, the grass-type Pokemon don’t really resemble potential food-type plants.)
As to the OP, Pokemon are in a rather nebulous nether-region between person, pet, and work animal. But, one point all of those categories have in common - for moral, and practical reasons, you don’t mistreat them. This holds in the case of Pokemon, particularly in the anime.
In the pre-GBA games, by definition, any Pokemon the player uses will be a fighter, but in the anime, and even in the background of the games, there are Pokemon with non-violent natures, who will be entertainers, or assist their Trainers with their work, or simply be companions, depending on the nature of the Pokemon and Trainer - a little of this also leaked into the actual play side of the games in Generation III with the introduction of Pokemon contests - but you can still only groom your Pokemon as competitors, rather than workers, or non-competitive entertainers.
Battling, due to the nature of Pokemon, and the Pokemon/Trainer relationship is more like boxing than dog fighting. Something all involved enter into willingly.
In the anime, attempting to get a Pokemon to fight when it doesn’t want to will be frustrating at best, dangerous at worst - for the Pokemon, or, if it’s like Ash’s Pikachu or Charmeleon, for the Trainer. This is only shown occasionally - Ash’s misadventures with his more intractable Pokemon, mostly - but it exists as a background note in the series. Even if it’s not of the sort of nature to turn violent against it’s trainer, and doesn’t die, the games show us that causing a Pokemon to dislike you yields sub-par results in training, so even a Trainer who doesn’t feel a moral need to treat his Pokemon well has a practical incentive to do so.
Conversely, refusing to let a scrappy Pokemon fight is also intensely frustrating to the Pokemon, and bound to put a strain on the relationship between Pokemon and Trainer. This facet of things, I can only remember being addressed once - a Trainer adored her Pokemon (I want to say it was a Snubull, but it’s been too long since I saw the episode - it was small, and I think pink, but that only narrows it down to a handful) and didn’t want it to get hurt, so she never had it fight - it, however, wanted to fight, so it ran away repeatedly, until Ash & co. found it, and sussed out what it wanted, so its Trainer let it fight to its heart’s content.
There are other Pokemon in unambiguous Trainer/Pokemon relationships whose trainers don’t make them fight - James’ Chimecho, for instance - but they generally don’t mind. It’s all about recognizing the Pokemon’s nature. (Meowth of Team Rocket is a very strange case.)
As to Pokemon in Pokeballs (Heh, balls </is twelve>), clearly, it’s not too terribly unpleasant for them, as their affection for their owners continues to grow while in them. But we don’t know exactly what it’s like inside one.
We do have enough evidence to convincingly speculate, however. We know, from Bill’s PC, and it’s variants and derivatives - and the existence of Porygon - that Pokemon (and possibly people) can exist as data. The visual effect of using a Pokeball - and the fact that the Pokeball is several times smaller than all but the smallest Pokemon (and even a Skitty would find a Pokeball-sized space a tight fit under normal circumstances) - we can safely assume that’s what’s happening inside a Pokeball.
As events outside the Pokeball effect the Pokemon inside - up to and including prompting evolutions - and effects of burns, or poisoning, continue to advance, we also know they’re not in stasis in there, and have some awareness of the outside world.
Now, we come to pure speculation.
My thought on the nature of Pokeballs, is that they put the Pokemon in a simulated environment similar to its natural habitat. Further, as the Pokemon in a trainer’s party can have an effect on each other, I propose that all a trainer’s Pokeballs are linked in a network, allowing them to interact with each other and the trainer.
Yes, I have given way too much thought to the subject of Pokemon.
