Sora doesn't kill anything. The hearts are released from darkness( other words purified of darkness. Sora does know this. That is why he attacks the heartless without worry. Remember Sora wasn't dumb until KH2, even then) and if the body, the heart comes from, isn't a Nobody it goes back to it. Completing the human that once was. You can actually find proof of this in KH at Traverse Town.
As for the Nobodies. They were bad. Just because they don't have hearts doesn't mean they can't be bad. Their cause was bad. The fact they were going around turning people into heartless is bad.
The fact they were collecting hearts was bad.
Think about it, we don't know what would have happened to the hearts after
Xemnas and the others made themselves whole.
Sora wasn't even going after them. Yen Sid and the others just wanted Sora to be on his guard and to know what he was going to be dealing with in case he ran into Nobodies. Nobodies are not always nice like Namine you know:
Saix sure didn't seem to hesitate to want to destory Sora.
Since he was no longer in the Organizations best interests. Besides, after a Nobody is beaten up. It fades back into Darkness. There it waits for it's heart.
You know the Organization had no intention
of finding their original selves.
No they wanted to be their own independent being.
Leaving their true selves in everlasting Darkness.
So, yeah, it was completely right Sora did all that stuff.
Besides, what else is Sora suposed to do. Let the Nobodies and heartless keep destroying worlds and creating chaotic ruin. Yeah...
Finally, I will speak of Roxas.
You can not count when Roxas was in Twilight Town 'cause at the time he didn't know he was a Nobody. He tought he was whole. So he lived out everyday life as a kid. Of course, when he retained his memories, he grew hateful, bad tempered, fit- throwing, ect. A lot like how he used to be judging by the way he acted toward Riku. What about Riku? Roxas sure was quick to try and murder him off. Roxas sure wouldn't have hesitated to kill DiZ. Actually he didn't. Roxas would have killed him if circumstances hadn't been as they were. Roxas would not have cared either. This is a bit of their conversation:
DiZ: Well, if it isn't the Keyblade bearer.
Roxas:Who are you talking to. Me or Sora.
DiZ: To half of Sora, of course. You reside in Darkness. What I need is someone who move about in the realm of light and destroy Organization 13.
Roxas: Why? Who are you?
DiZ: I am a servent of the world...(he laughes) and if I am servent that would make you, a tool at best.
Roxas: Was that supposed to be a joke. Because I'm not laughing.(attacks DiZ)
DiZ: My apologies. This is only a data- based projection.
Roxas

screams and starts atcking it nonstop)
DiZ, when Roxas is done: Come, over here.
Roxas: I hate you soo much.
DiZ: You should share some of that hatred with Sora. He's far too nice for his own good.
Roxas: No! My heart belongs to me!(attacks DiZ again and DiZ dissapears)
Sora isn't dirty minded. I don't know where that came from and sure he is a bit disresectful, but what boy his age isn't. Sora is just being a guy. A pretty decent one I might add and he is sort of acting like a lighter Riku. Which is kind of weird. all I'm saying is that Roxas isn't lighter than Sora. He has his moments, but truely Sora is the light, pure one here.