Sarah did warn him of the likelihood of Fulcrum torturing him. I think Chuck isn't ruling out the fact that he could end up dead or being tortured. Both of which would be worse fates than imprisonment.

Poor Chuck though. I think Sarah's line summed it up best though about giving someone a life sentence just for being a good person. That's sorta what his situation could turn into.

Yeah, I think you're right about Ellie's view of Sarah.