I guess we all forget the fact that it's ultimately the Pokemon's choice to battle. Disobedience is an issue in the Pokemon world. Of course, there's always those who "force" their Pokemon to battle through abuse, but honestly, that's just a reflection of our world. There are always pet owners who abuse their pets.
Also, trainers are not the only type of competitors who use Pokemon in the Pokemon world. As introduced in AG, there are co-ordinators, people to enter their pokemon in beauty, intelligence, cute etc. contests.
I agree with you about the bonds being different in Digimon and Pokemon. As you said, Pokemon don't have the same connection/relation to their trainers as the digimon has toward Taichi & co., and the relation between the digimon and their partner is pretty much the plot behind the plot.
The kids were not fighting for a more justified purpose. Killing is not justified. At first, we thought nothing of it, because they're the "bad guys." Either way, it's still life, as we see/hear explained in 02.
I'm not saying Pokemon battles are justified either, because, they're not. I understand what you're saying though, compared to Digimon Adventures, Pokemon battles are pointless. Although, there's something we should consider:
Using Bulbasaur as an example, it wanted to battle due to its past. At one point, Bulbasaur was the protector of a village. Due to the fact that it wasn't strong enough, he almost couldn't protect those who were important. Bulbasaur is only fighting to become stronger so that it can protect. It's fighting for a personal goal.
That's why I think people need to realize that Pokemon and Digimon are two VERY different shows. They're fighting for different purposes. Pokemon focuses on fighting for their goals/dreams, while Digimon focuses on protecting what's important to them.
@Fresh_Coffee: As Kihaku said, having courage isn't just for one. There are hundreds of other anime before Pokemon and Digimon that focused on courage and friendship.