Yes, intent matters.
Football is inherently a violent game. You always derive a benefit from knocking a player out of a game. That being said, that does not make organized bounty pools (especially those that coaches participate in or organize even) OK.
From what I heard, they even had a specific incentive for having a player carted off. If true, that is disgusting and well outside what the bounds should be.
The fact that some people (not saying anyone here) are trying to paint those who oppose this practice as naive is ridiculous. For one thing, "everybody's doing it" is not a defense when you are stupid enough to get caught. We can only deal with those that we know about, I'm not giving the Saints a pass because "everyone does it." When another team gets caught, then we'll deal with that one too.