I like Jonathan better than Andrew (Four characters in-between the two on my favorites list, actually), but Andrew had a bit more to offer. Jonathan's story arc basically ended with his revelation and subsequent murder.
Anyway, I can't see Jonathan pushed by The First into killing Andrew.
Andrew is more gullible than Jonathan, more unfamiliar, more willing to commit crimes, therefore more likely to do The First's bidding. Besides, who would The First become to make Jonathan do those things? Is there anybody in Jonathan's life on the show who died and meant something to him? He didn't like Warren at all by the end of Season Six, he had no parent figures or real friends, and the few 'friends' he did have, or at least people he was friendly with, kinda rejected him after his time with Warren. Andrew was his only friend, but he isn't dead. So the concept of it being Jonathan surviving wouldn't have worked from a storytelling point of view (If it was a matter of who deserved it more, Jonathan should have lived, but then Andrew wouldn't have been able to develop over the season. In a way, Jonathan indirectly help to develop Andrew's life).