John left dean because he knew the demon had returned and would likely go after his youngest Sam. He knew that if he went to Stanford Sam would not leave but if dean went Sam would go with him because he could never say no to dean as a child.

When john found out about jess he wanted to go straight to Sam, but he knew he couldn't. He needed to find this demon before it hurt his family any more then it all ready had. He has all ways want Sam to under stand why catching and killing this demon was his top priority, but not like this not because he lost the girl he love the same way hi lost Mary.

He knew one day he would see his sons again but that would not be any time soon.