Yeah, I think you’re being too harsh on him. In Refrain, we see him as a broken man, a shell of his former self. He clearly regrets his actions in Rin’s route, but everything he does is for the sake of saving Rin and Riki. The whole point of Little Busters is to make Riki and Rin strong enough to face the cruelty of the reality that faces them. Kengo wanted to keep on having fun forever, which is admirable itself, but to do that is to completely reject reality. Kyousuke wanted Riki and Rin to move on from the sad reality, not run away. To that end, he did everything he did. He put Rin (and Riki) through a trial to overcome adversity, believing in his decision. He didn’t do it to antagonise anyone, he just made a mistake. He manipulated Kengo because Kengo stood in direct opposition of him and was preventing him from accomplishing his goals. He was willing to make an enemy of even Riki and Rin, the people he loved more than anyone, if it meant saving them. If that’s not selfless dedication, I don’t know what is. You can’t just ignore that.
As for manipulating Masato, I don’t believe that one bit. Masato remained a neutral party. I’m sure he joined with Kyousuke in the baseball match because he wanted a fair fight, not because he was being manipulated. He’s not that much of a fool. Not that it was fair in the end, but I’m sure Masato’s actions were of his own will.
In a way, he’s both a villain and a hero. But what’s important is that everything he did was for the sake of Rin and Riki. That’s a villain I can get behind.