So I finished Cass's quest peacefully and gave the info implicating Alice McCafferty and the VanGraff's to Rnger Jackson. Now when I go to Freeside, the VanGraff thugs outside the Silver Rush attack me. Is this supposed to happen even if you go the peaceful route?

Thanks!

Yes, if you complete Cass' quest the peaceful way, the Van Graffs will instantly be hostile to you. Not that they were good merchants anyway :spotted owl:

Since Cass's quest is already marked as complete, will I still get the good ending for the NCR if I now go kill McCaffert and the VanGraffs?

You will still be able to get the good NCR ending, the two quest lines don't affect each other. I would also definitely recommend killing the two ladies with Cass in your party. When you kill one of them she will come up to you and tell you to make up your mind and to go kill the other one.When you have killed both of them it will reward her both of her quest perks, thus making her a force of nature with a Brush Gun.