Editors of haiku magazines and books usually set the prose parts of haibun using justified lines, and I've never heard of an author objecting to this.
I would like to suggest a beneficial change to this practice. It's the authors, not the editors, who should have the right to determine where line breaks in prose will come, just as they do when their haiku are set.
But to earn this right, authors need to develop sound reasons for asking for lines of prose to be broken where they want. One reason might be to keep phrases intact, and so give the reader more of an impression how the writer would read the piece aloud. A more imaginative and creative reason would be to use line breaks occasionally for the purpose of enjambment (in the way writers of 'free verse' do.) Enjambment may create suspense, emphasis, or surprise.
If writers develop some skill with these devices it might perhaps contribute to distinguishing haibun prose (or indeed 'poetic prose' in general) from straightforward prose.
First published in Blithe Spirit V15, N3 (September 2005).