To be fair, Bones didn't really think of anyone in anything more than a platonic capacity other than Jim, the one-night stand with Faith aside. He was well and truly hung up on Jim. Right now though, Jim was causing him a good deal of distress, and he needed the reassurance Nyota was providing. It was nice. Strange, considering he and Nyota hadn't been close before coming here, but nice.
He turned to face her, returning the smile with a small one of his own and holding on to her hand, amused suddenly by the idea of Jim's reaction if he ever found out the two of them had shared a bed. The amusement promptly faded as he thought of his lover's reaction to Faith. "The irony is that I put up with what he does, but he'd have a fit if he thought I was sleeping with anyone else. The difference, of course, is that I wouldn't." He smiled wryly. "But you're right. It will all work out eventually."
He paused and shook his head. "If by 'or another' you mean you beating him until he comes to his senses, please don't. Jim just needs time, Nyota. And I can give him that." He looked resigned. "I can be patient with him."