Well, he didn't want to kiss her. She initiated the kiss, then he gave in for a couple seconds, before standing up abruptly.
I think we are supposed to see that he is riven by guilt over his "carelessness" that destroyed his family, and that he is too responsible and disciplined to play with her affections when there is no hope. But... there is a tiny sliver of hope (he thinks) because maybe the alternative treatment will cure the syphilis. He says that "all things might be possible in time but time is not with us... and my adversaries are powerful." Meaning, the devil, temptation, sin, and the earthly toes he is stepping on.
He seems to have completely forgotten that she was ready to marry someone she didn't love in order to help her brother. If he's the reincarnation of Sharpe, he's not any smarter about women. LOL