I'm not sure being turned in to paste would be considered throwing a bone, though.

Jojen Paste is just theory at this point, though. At best, it's implied that his blood is in the paste, but it's far from confirmed that he's dead in the book.

And by Meera taking over Jojen's place, I meant the eventual return to Greywater Watch (the Reeds' home) and whatever was supposed to happen to Jojen there. Although maybe in the show they'll have Meera avoid death somehow?

Well, if I recall correctly, when Bran asks Meera where Jojen is, she starts crying.  With the unknown but fair amount of time that has passed, and I believe everybody else that was there is still there, and that Jojen knew he was going to die, it's pretty heavily implied that yeah, Jojen sacrificed himself for Bran to be...whatever he becomes.

I think he also sees or hears something that in the past men were sacrificed for this?

It's not 100% clear, but it's about as clear and implied as a certain other character's parentage.

Jojen's health was already failing as they neared the cave. 

The paste is probably just weirwood sap, which is red and constantly referred to as blood-like.

Getting killed in the show and then fireballed post-mortum is a pretty good indicator that his sole purpose was to get Bran to the cave--at which point he probably finished dying.  The paste theory either wasn't true or is vastly unimportant.

(The only Jojen theory more ridiculous than Jojen-paste is that Jojen is Meera's dad.)

Probably not vastly unimportant:  Greywater Watch and Howland Reed, AKA, the only person who knows Jon's true parentage.  And the key to that particular plot?  Is Meera.  So her getting pasted is also prrrrrretty unlikely.