The movies made it seem like Thor and Loki had a good relationship before everything with the Avengers happened, but Loki and Thor have been butting heads for a really long time in the comics. Like since the 70's story arcs. Loki never actually wants to outright kill Thor, and when given the chance he never does it. I don't think Loki wants Thor dead, just out of the way, but not too far away. He's a complex character which makes him so much more interesting and adds a level of dimension to Thor's character; he knows Loki won't kill him, and doesn't really want to hurt him, so he can't outright hate Loki, but he's forced to fight him. This sums it up pretty well, and it's freaking adorable.