This is a pretty intricate match up, actually.
IMO, it's dependent on Kakashi's speed with Kamui, and how many times he can use it before straining himself. If he's faster than Amaterasu (usage speed) and can use it 2-3 times in rapid succession, he could take the win.
It gets confusing during the War arc to evaluate this. How many times did Kakashi use Kamui in total? How many times was that due to Kyuubi chakra? These are questions that need to be ironed out before determining which feats are rightfully his and his alone.
Itachi's genjutsu (except for Tsukuyomi) won't work on MS Kakashi, so there's a big disadvantage for him right there. And Kakashi probably won't make the same mistake he did in their fight in Part 1, so Itachi won't be able to catch him as easily.
Anyways, if this was against pre-War arc Kakashi, it's Itachi's win. So unless he has the improvements I listed, the outcome wouldn't change.