The Echo Station interview says, quote:

ES: How did Lucasfilm react to your plans to establish a final treaty of peace between the Republic and the Empire, effectively ending the conflict forever? Did they have any initial objections to this?
TZ: I had certain amounts of resistance from LFL to both the Luke/Mara and Imperial/Rebellion resolutions. (Particularly the first, as I recall) But I felt strongly that both plot threads needed to have closure, and made it clear that unless I could do both I wasn't interested in doing any more Star Wars novels. That wasn't a grandstand play, incidentally; if they'd turned my down we would have gone our separate way with no hard feelings. I simply wasn't interested in doing another Star Wars book just for the sake of doing another Star Wars book. Fortunately--because I really DID enjoy doing the books--they decided to trust me and gave me the go-ahead.