I think there is a difference. Of course, if you aren't too much about role play and more about experience, you'll just kill everybody. But basically, you can reach the core by taking a left or going on the right. One of them will take you to your friends and then, to Sion, and Kreia, the other one is just a kill-fest. Alas, that is what I remember, I almost never get to Malachor in my games