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I know we're lead to believe he did. However Lionel seems to say that he didn't, and I know you can't trust him, but he did get get redeemed later, & while e did accept the fact that he had done so much wrong in his life, he still said that he didn't kill his parents? When he was getting taken out of jail he said something like "I'm not guilty for the crime of which I'm in here, but I am guilty of so many other crimes". So did he kill his parents or not? It's never really clear? And if he didn't, why did he confess to Chloe Sullivan when she was on truth-factor that he was the one who murdered his parents?

You kinda answered your own question. When he said he did it, he was unable to lie do to Chloe's power. When he said he didn't, he was under no obligation to tell the truth.

Honestly, I think the writers messed up with this, but all in all there is no reason to believe he could somehow resist Chloe's power and lie to her. The only one who could do that was Clark due being an alien