I'm not saying Jon is completely innocent by any stretch. His actions have indeed caused deaths. Uniting Northerners with the Wildlings though I don't think was possible without parties on either side dying. He definitely could have made better choices though and even admits that himself.
Theon: "Every step you take is the right step."
Jon: "It's not. It may seem that way from the outside, but I promise you, it's not true. I've done plenty of things that I regret.
Theon: "Not compared to me, you haven't."
Jon: "No, not compared to you."
He's as close to 'good' as you're going to get with this show though and far from evil.