True, but that's only if Minato delays his teleportation like he did against Obito. If he does it instantly then he won't lose any body parts.
When the Gedo was summoned by Madara, it wasn't instant, it still took an extra second to leave Obito's body which gave Kakashi the opening to take just its arm off. Minato doesn't have that problem, he teleports in the blink of an eye, Kakashi's Kamui is fast but not FTG fast.
To be honest, I think Kakashi has a chance because he knows Minato's abilities better than anyone. If it was the same scenario as Minato vs Tobi, and Minato throws the kunai towards Kakashi instead, Kakashi easily warps it away. Since Kakashi knows he warps to those kunai's he just needs to keep his distance and warp every Kunai thrown at him, or deflect them with his own Lightning Kunai.
Problem is, what happens if Mianto scatters all his Kunai around the battle field? He can't Kamui all of them.