Why didn't Jesse kill this character

Breaking Bad already showed us that Jesse was broken by the gang, hence him failing to kill Todd now even when he has the opportunity.

It is even explicitly stated in an earlier scene in this movie that if Jesse tries anything, then Todd will need to visit Brock. Todd's death or disappearance would inevitably cause the same.

As Alan Sepinwall writes:

So when Jesse takes Todd’s gun out of the glove compartment, we know he won’t shoot the pasty monster and make his escape. Suspense isn’t just dependent on surprise, though, but on context and execution. That scene is unbearably tense not because we think Jesse might pull the trigger, but because we know he won’t, and can’t stand to see how or why.

Once, in the original series, Jesse described Gale as a problem dog who had to be put down. Several seasons later, Walt objected to Skyler describing Jesse as a rabid dog who needed the Gale treatment. Here, Jesse isn’t a problem, and he isn’t rabid. He’s just a dog who’s been broken by a cruel, unyielding master who isn’t afraid of that gun, because Todd knows his little pet could never use it against him. Jesse has the ongoing threat against Brock to think about, but beyond that, Todd has just relentlessly ground down his humanity into paste.

The part of Jesse Pinkman that would be capable of pulling the trigger, driving back to Albuquerque to warn Brock, and heading for parts unknown has temporarily left the building. The ongoing trauma of enslavement has left him a shell of the outlaw he once tried to be. It’s terrifying and heartbreaking to watch, even as we know that Jesse eventually chokes the life out of this son of a bitch.

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.