I think Matt definitely was a minion, at least when he thought it was still Nathan. If Claire had left, he would have asked Matt or the Haitian to find her, I'm pretty sure. But that's just my hunch on the psychology of a character in a TV show. I'm supposed to be studying law.
But everyone thought Clair was dead. The only reason Matt found her is because he read Bennet's mind. I don't think Matt turned her over to fake Nathan thinking Sylar would kill her. I think he like every other person was afraid of people using their powers for evil...which is why he is working for homeland security. Sylar is as evil as they get. He would not help him. Plus Sylar is supposed to be dead. Everyone thinks he is the one who blew up New York. So he can't have minions if no one knew he existed.
Sorry, I think I didn't make myself clear. What I meant was Matt was a minion of Sylar's because Matt was ready and willing to follow his orders (because he thought Sylar was Nathan, his president). If Sylar had in fact not killed Claire, and Claire had escaped, I believe Sylar would have called Matt and said something like "Claire is feeling a little overwhelmed about our reunion. I think she might have run away. I'm really worried something might happen to her. I need you to find her." Matt, trying to impress his boss and perhaps even genuinely worried about Claire's safety, would have had to look for her. I was only being tongue-in-cheek when I said the whole "minion" thing. My point was, Sylar would NOT have let Claire go without some sort of effort to keep her.
Additionally, I don't think Matt just found out Claire was alive. If you rewatch, when he first talks to Mr. Bennett about the Underground Railroad thingie, Matt refers to the fact that they're both hiding children, and says something like "Except mine isn't the President's daughter." I'm pretty sure Matt had known about Claire for a while, but had kept quiet because Bennett was also hiding his son and his wife. As soon as he realized he'd lost Hiro and was going to be in trouble with Nathan, he decided he needed some sort of consolation prize for his boss so he went to get Claire.