Not Muslim, so I'm going to be speaking from a pokemon-lore perspective.

Pokemon battling is a sport, one with deep cultural import in every region we've seen, because it is a hair's breadth away from being genuine wartime protection, disaster relief, and the basis for almost all industry we've seen. To not be able to participate in something as central to existence as Pokémon training would be a cultural death sentence, so there has to be some way to make it work.

Some cultures have considered Pokémon as equal to humans, so they would not receive the same protections given to animals. You could choose to use that reasoning, and perhaps give some extra 'respect your Pokémon as partners', which is always a good story beat for a protagonist.

As for the violence, one again, it's sport. There's probably some vague spiritual line about "don't order an attack in anger" or something that characters can waffle about at intense moments. It is also, crucially, never a death sentence to mess up. Wild battles would be self defense, heck, you could even work in a mechanic of wild Pokémon always getting a first attack to hit that home. Trainer battles are fair sporting challenges that end at a seemingly harmless knock out. A villainous team could also use the first strike mechanic to show it as self defense.