It's almost as if wartime collaborators seeking to follow up on an attack that killed 3000 civilians are treated more harshly than freelance terrorists.
As I recall, the evidence against Rudolph was a lot less clear-cut and the investigation had been bungled previously, giving him a good number of openings at trial to poke holes in the government's case. Given that, it made a lot more sense to offer him a plea and ensure that he went away forever. No one was finding Tsarnaev innocent.
Nobody's saying Tsarnaev was innocent.