Specifics worked for John – identifying the issue, determining what he could and couldn't do and then doing what he could to the best of his ability. The issue here wasn't entirely Mary, but the whole dynamic of family. He couldn't walk away from his sons, he realized not even in such a small way as this, so now it was time to figure out what would make it easier and then get it done.
"Nah, for now, we'll stay just as we are," he said, squeezing Dean's shoulder in a silent appreciation for what his son had just done, not just for himself or John or Sam, but for everyone. "Safer that way and that's the most important thing, that everyone stay safe." More important than anyone's comfort. They had time to think about comfort first after these demons were gone for good. For now, staying close, the girls not going anywhere alone, always having either him, Dean or Sam in the apartment, was the way to go.