I was under the impression that they couldn't fuse because he was a jinchuriki period, not because he and Kurama were at odds..
Besides he doesn't need them. He has surpassed Jaraiya's SM because Jaraiya was nearly a toad when he went to SM (a sign that he hadn't mastered complete stillness) while the only thing to change on Naruto was the little mascara at the corner of his eyes, LOL!
If it was because he was a jin, then they wouldnt have even tried. Simply though, kurama got jealous, and did not allow them to fuse.
Now that kurama is more friendly, he may allow them to fuse. But jman, mastered the stillness, but he did not balance his chakra correctly, and had to much nature energy, so he was toadlike. Both naruto and jman mastered stillness(plus jman has had practice with stillness, when peeping at ladies.) The only difference, between naruto sm, is naruto mastered the balancing/molding of nature chakra, while jman did not fully master it.