But he doesn't kill him and instead settles in for a pizza and cold beer on the ride back to his cage.
Why did he choose a pizza and beer instead of his freedom?
I feel like you've very much misread Jesse's response. He is in tears because he realizes that anything other than acquiescing to Todd will mean Brock's death. He doesn't settle for beer and pizza, he doesn't want to go back. But he has to do what Todd says if Brock is to survive.
This is emotional torture at its finest. Jesse is so broken that even with a clear path to freedom, his emotional attachment to Brock is keeping him in that cage almost voluntarily. And it breaks him when he realizes that (which happens seconds before he hands the gun back).
Todd pointed this out right when Jesse is let out of the cage: any misbehavior leads to Todd visiting (i.e. killing) Brock. If Jesse kills Todd, Brock will simply be visited by another gang member.
Yes, Jesse could've hidden Todd's body as they were already in a prime location, but as long as the gang returns to the hideout and Jesse (and Todd) is missing, Brock will still end up dead.
But later in the timeline of Breaking Bad, he actually does kill Todd by choking him to death and fleeing in the car roaring his freedom. What changed after?
Walt killed the gang, so there was no one to go after Brock anymore.
Even if a handful of members survived, they would be on the run and laying low. The odds of them deciding to kill Brock at that point is next to none. Jesse's escape isn't the most pressing issue for them anymore.
