The Van Graffs aren't exactly known for their good business ethics, considering the way they operate, it's no surprise that some people would hate them, and want to even things with them, we can see this in the task they give you to perform guard duty for them,
Spoiler where one of the people who tries to visit the store, if you let him in, will activate an explosive, blowing them up. And if you insist on searching him before he can enter, he attacks you and you can find a revenge note on his body.
I figure it's no surprise that many groups would want you to kill them.
So far, though, the only quest I've recieved where I'm told to kill them is Cassidy's, and in that quest, you can just kill them or you can search for evidence to incriminate them, so far, I've yet to complete it either way.