Pain didn't kill her. A lot of his bodies are dead, so he needs new ones. He looks at her, looks at Naruto, realizes her body is out of Naruto's vision, so he plunges the black sword into her body while missing her vitals.

The black sword is made of the same material as the chakra receivers - Hinata is alive, but as Pain's new servant.

Pain also knows what Hinata's abilities are due to his past encounters with Konoha, and he's going to need it to "see" the Kyuubi's chakra. IE - where to attack, where it's hiding, any weaknesses, and how to capture it.

Pain can only capture Kyuubi after "extracting" it out of Naruto. Pain's servant, the paper-girl (totally forgot her name), warned Pain that he used too much chakra already - ie. he doesn't have enough to capture a released Kyuubi in his current state. The whole "stabbing Hinata" was just a ploy to have Naruto release Kyuubi without having to do it himself. Now he has another body that has an extremely useful eye ability to help him.

Also, when Pain says that "My pain is worse" in the last panel, he says that because he was forced to kill his own parents by Konoha ninjas. This is probably why we're seeing Shikamaru and his father recently. Shikamaru's dad was the one who forced Pain to kill his own parents.

Pain will try to get Naruto to kill Hinata, to have Naruto "feel" his pain of killing a loved one, and Shikamaru's dad will find the real Pain just in time.

kanoha ninjas making him kill his own parents

I do not think Pain's corpse are so easily obtained, I think that it takes longer than it seems for him to actually set up a corpse for him to use ( i mean like a long time). Second, Pain's eyes are WAY better than Hinata's bloodline eyes, so i don't think that he would use Hinata for that very reason. Another thing is that, Pain does not seem scared at his Kyuubi at all , so he is confident in his skill,the only thing i can think of is that he might use Hinata's body for a shield.