If Muu becomes invisible he can't use Jinton. By using jinton he must accumulate chakra and with the sharingan Kakashi could notice it. Kakashi makes a raiton kage bunshin and hide underground. The clone will try to notice Muus position the same way like he did against the invisible guy in Kakashi gaiden(by smelling and hearing sounds). In invisible mode, Muu would try to attack in close combat. If he hurts the raiton kage bunshin, he will be paralyse. At that time, Kakashi could come out and finish the fight. Guy could also go 6 or 7th gates and finish him with a combo at that moment
But i think Muu won't use his invisible mode while fighting(cuz it has a great advantage to surpise an ennemy, but you can't attack using ninjutsus or things like that). So during the fight, most of the time, i think he won't use this mode. He will probably want to kill Kakashi and Guy with Jinton. If he manage to spamm it really quickly he wins. But Kakashi could actually decide to launch kamui quickly(while Muu prepare his jinton) to finish him before that, the same way like against Deidara.
Anyway every time Kakashi has no other choice, he uses kamui and fighting Muu who can fly, being invisible, spamm dangerous techniques such as Jinton, i think he will decide to use it. Even if he doesn't use it from the start, after one use, he will have no choice but to have to use it