I think the important thing to consider here is that Tom was "not a wartime consigliere" as was stated by Micheal later. He wanted to do whatever he could to avoid a full out war. In that sense he and Sonny were like opposites with Micheal somewhere in the middle.

Tom told The Don he thought they should make the deal before Vito was ever shot. After he was shot he knew Sollozo was making the right suggestion but knew Sonny wouldn't go for it (or Luca Brasi, as he said in the car) because of hot headedness.

I don't think he went against the family he was just a lot less effected in a personal sense by the Don's attempted murder. He was still able to think of things in a business sense were all Sonny wanted to do was kill kill kill in anger. That's why Tom made such a great lawyer.