I'm not saying that there has to be a huge balance between good and bad or that they wouldn't have a good reason to justify attacking us humans(because we can be bad), I just personally find it slightly appalling that we would be at fault for nearly everything truly bad that goes on.
An interesting thought that came into mind is how those legendaries with such high thinking capacities are in a way similar to us humans in that we've grown far more aware of things than the average animal(evolution-wise, but that's for another topic really). If we are capable of these so called wicked deeds(or at least influencing average Pokemon to carry out our wishes, whether they be good or bad), then no doubt a legendary(if only one) could be capable of the same thing.
For all we know, said Pokemon could be all but banished from our world because of the good-natured ones forcing it to flee, which could be a reason we have yet to come across it or everyone has all but forgotten about it(except maybe those who caused it to flee to begin with, who would be more than happy to forget it if they could anyways).
I can see where you are getting at but this is where I'm coming from.