To me, Hinata always had her heart in the right place, but always went about things the wrong way. She takes Naruto's nindo and uses it to justify near-suicide. I laughed my butt off when Pain one-shotted her because I figured that she totally deserved that for doing something so outrageously stupid and this was the author admonishing her. I can understand wanting to protect the one you love, but what she did was blatant suicide. In fact, when Pain stabbed her, I thought she was dead. Then later we found out she survived and in that same scene we have Sakura thinking to herself on how Hinata really shouldn't have done what she did as if the author is trying to reinforce the negativity of her actions and almost condemn them.
I had honestly thought Hinata had at least learned something from this experience, but then we have almost the same situation happen yet again during the war. It's contrived enough that Hinata was even in that position in the first place; that whole "we're the hyuga, we'll protect Naruto" thing, because there seriously wasn't any one else who could have protected Naruto out of the entire shinobi alliance.
Regardless, yet again the author makes Hinata pay dearly for trying to protect Naruto. Instead of a near-death, she gets hit with the death of her closest relative. Killing her at this point would be a mercy because now she has to live with the fact that she got her cousin killed. Survivor's guilt can be a kitten.
Honestly, killing Hinata at this point would be like killing Kakashi. They already had their moment of dying, an actual death would cheapen it. Then again, I feel like Hinata surviving her encounter with Pain cheapens her confession because they no longer are her last words to Naruto so they lose some meaning.
I'm not bashing her or anything, just saying that there's no point in killing her at this point, it honestly wouldn't change much.