Yes. It's hard to look at Booth chronologically and not think they made up stuff about his family as they went along. He mentions a brother in Season 1, yet we don't see him until Season 4. Similarly, any mention Booth has made of his father up to the end of Season 2 is positive. He even says he loves him and that they were tight. All as you say to encourage Bones to feel affection for her own father. That is finally resolved in The Verdict in the Story.

Also, Brennan does tend to dismiss things that are important to Booth: religion, sport, family, love. He really has his work cut out to keep going with her as long as he does.

Yes, Booth and the removal of Zack does have repercussions!