Kakashi would win.
1. kabuto has : healing. paralyzing jutsu. and dead soul jutsu.
2. kakashi has : 1000 jutsus. sharingan. rakiri. very intelligent on the same level as kabuto. kakashi could just copy his movements. use hypnosis genjutsu. his summoning dog jutsus. He's quicker. Stronger. can avoid kabuto's hits by reading them with the sharingan.
3. Kabuto was only able to kill Anbu's because of the dead soul technique by impersonating an anbu (How cowardly but smart though. He wouldnt face them one on one though with out impersoanting them.)
kakashi would basically run over kabuto one on one if it was a fight to try to kill each other not stall. but like I said kabuto is smart so he would probably run away to avoid being killed by kakashi cuz he knows he's outclassed and outmatched xD
Kabuto would put up a fight but Kakashi wins. Kabuto is no match for a sharingan no matter if kakashi isnt an uchiha. In part 2 kabuto is basically a stepping stone compared to mangekyou. he is no match for mangekyou of any ability, shape, or form, eternal and non eternal
Now it would be interesting and something to talk about if kakashi didnt use sharingan. Now different story but kakashi would be on the verge of death but he would win still because then they would be an absolute equal.