Rule of thumb: Do what is best to protect Clem
Moral Code: Don't kill any (alive) people.
I figure if Lee doesn't kill any (alive) people then when the truth comes out at the end that he murdered someone then the folks will look kindly on me when they see I have not been going blood thirsty hacking at everyone (alive) that I could. Would make them trust Lee, despite his past.
And protecting the girl is a no brainier. It's really the only think making Lee human and not a freed convict.