How do YOU know it's against their will? Most Pokemon are quite intelligent, despite their lack of human-speech communication; the trainers don't FORCE them to battle, they act as the team's director/coach. And, this: seriously, do you REALLY think ANYONE could FORCE a being that can MAKE A BLACK HOLE, or one that could just ELECTRICUTE/BURN/FREEZE/etc-you-to-death to do ANYTHING it didn't agree with?!). Sure, there's SOME (like... maybe... Magikarp.) you could BULLY into working with you... but when they evolved... they could pretty easily kill you in a rage. Of course, just like humans, you could traumatize/manipulate them into staying obedient, but just like reality, there's good and bad people of all types and extremes.
Also, it's stated IN THE GAMES that humans and Pokemon come from the same evolutionary roots in the first place (not so badly as humans and monkeys, it's supposedly somehow closer), and that in the not-so-very-distant past of Pokemon's world/universe, they were considered fully equals, working together in everything from farming to war.
