"Defeated" does not mean "killed". The akatsuki have taken down biju before. BM Naruto takes this for a multitude of reasons.
-Kurama is still a living being, he should have recovered his chakra since being sealed unless your gonna tell me he totally lacks mental energy now
-Even if he is lacking chakra, a jinchuriki is still the biju's chakra+the host's chakra. Kurama still has Naruto's chakra to make up for the difference.
-BM Naruto has a much better assortment of abilities: super speed, clones, summons, etc