Kakashi can't exactly end it with Kamui...
1.) Madara knows what Kamui is and how it works since he trained Obito.
2.) Kamui requires time with the target to stay in the same place till Kamui finishes. Madara is insanely fast. He was fighting KM Naruto with some ease.
3.) Kamui takes a ton of energy from Kakashi. He didn't come back from the other dimension just because he was slightly winded or waiting for opportune moment. He literally had no energy to perform it. He barely has energy at the moment to perform a single Kamui, so if he fails first attempt, Madara will just kill him to prevent further attempts.
4.) Black Zetsu seems to have control over Obito. That means if Kakashi succeeds, Black Zetsu can force Obito to go get Madara out (that is if Kakashi does it before Obito dies).
5.) Naruto's Plot-no-jutsu.