In the real world, I would side with Kilik. He's got everyone's best interests in mind and is content to stay in the shadows simply making sure that people don't get their hands on a dangerous power. Sora is just interested in his own power and doesn't care how many people die to get it. Of course, there's the argument that Kilik doesn't have the right to decide who can have power and who can't, but the police report that Kaito showed him shows that if there's already that many deaths resulting from what's pretty much just a rumor of the Sky Regalia, having it in the open would almost result in a full out massacre.
Of course, it's anime/manga so most people reading prefer the "I eat impossible for breakfast!!" mentality that Ikki has. I root for Ikki the most too of course, but I think it's far more interesting to look at Sora vs. Kilik because Ikki's attitude is just your typical shonen mindset that he has to have because he's the main character.