No Conspiracy Theory - They are a couple. They are in love.

I really appreciate this answer SN gave in an interview. The ambiguity prior to this interview was killing me!

Mega Buzz 5/24/2011 - S7 Bones :)

From this article here.

Why did Bones not show Booth and Brennan's hookup? Are the writers going to reveal that Brennan actually got pregnant by using Booth's donated specimen instead? — Melanie
ADAM: Executive producer Stephen Nathan likes your conspiracy theory. "Let's keep that one alive until next season," he says with a laugh. "Let's let people get all upset." In truth, Nathan says the writers were more concerned with feelings. "Whether or not we see them jumping around in the sack did not seem as important as the emotional acceptance of who they were to each other," Nathan says. "Moving into Season 7, [the pregnancy] cements their relationship and forces them to accept the fact that they are a couple, they are in love and that they will be moving forward together."