An unanswered important question

So the Middle East is in turmoil. Surprise! Who would have thought! I have a hard time deciding who I dislike the most. A terrorist organization that kills innocent civilians, or Hamas. I really can't side with an organization that has no respect for human lives. I understand the reality and the complexity of the situation, I just can't sympathize with any side. I am really divided over this. Deep down, I think Hamas is wrong, but Israel can't win my affection for this.

Now, while I was trying to argue this issue with a friend, an important question came up. How should a Country deal with terrorism? What is a State supposed to do when a non-government group decides to launch un-conventional warfare on its citizens? Peru dealt with Sendero Luminoso by crushing them like cockroaches, they caught his leader, and displayed him in a cage like an animal. But that brings other issues, I can't get to deep into it right now, but my point is that I don't think the means justifies the end. But I can't think of a way to solve this. What would be the best remedy?