Claire didn't say 'maybe they weren't having sex', but it wasn't because she believed strongly one way or another. It was that, to her, that act was interchangeable with what Sam and Ruby had been doing and to couch this in terms of "maybe it's not THAT" made it feel like it took weight away from what had been cheating, more potent because of the emotional connection than meaningless sex ever could be.
"They don't deserve each other," she said, passing the bottle to Faith without remark, "she deserves to be destroyed. He deserves... I don't know, maybe some people would say he deserves to be put down now."
She didn't believe that. She didn't want that, God how much she didn't want to lose Sam, even though to try and help Faith, it had meant accepting that she felt just as lied to in a different way and had judged herself because of it. In realizing that she now viewed Sam's assertion that she was his family as something that might only have existed in his addicted mind, she could understand why Faith questioned not only Sam, but herself.
That Sam would have been one of those people arguing someone in this situation should be put down, were it not him, it just hurt that much more.
But she wanted Faith still reacting, still talking, no matter how ugly or painful the reactions and words would be. It was why they were here in her house to do this, where no one could judge Faith later for things said in anger and pain.