|Booth, Brennan, and Christine|
Executive producer Stephen Nathan did reveal to TV Guide that Booth is "furious" and thinking "Isn't there some way she could include him? Why didn't she trust him?" Max Keenan did address just that, pointing out that he needed to be where he was to keep Brennan out of the system, where Pelant could easily get to her and do who knows what to her. Booth will realize that Brennan did what she had to, but you can't blame him for being angry with her for taking their daughter and just leaving like she did—even though she had no choice but to do just that.
Nathan did go on to say, "He realizes the only [other] way to keep [Brennan and Christine] safe would be to do something illegal like taking out Pelant. We wanted Booth to remain a good man. To put him on the run compromises his character and his job. So, when Brennan does return, [Booth] is still the honorable man that he's been for seven seasons." Though it doesn't sound like Bones season 8 will see the two apart for long, the threat of Pelant is still very much out there, and since Booth can't "do something illegal like taking out Pelant," it's up to the Jeffersonian team and Booth to do what they can to take care of him so Brennan can return home safely with Christine again. If anyone can do that, it's them. Considering no one quite knows what Booth went home to—it certainly seems like there could be a bomb in that alarm clock, plus there's video footage of Pelant there—it doesn't seem like it's too much of a stretch to imagine they can build a case against Pelant.
What makes the series so good—and continues to make it so good even after Booth and Brennan got together—is those two working together and neither afraid to say what they need to in a certain situation. So it wouldn't be surprising if Brennan brings up that Booth should be mad at her and he explains he gets why she left, or for Booth to tell her he was mad before she mentions it herself. Either way, seeing Booth reunite with Brennan and Christine is something to look forward to in season 8.