If he wants to live yes he will, being in the air doesn't change anything, not when this is a desert. There is nowhere for Mu to hide so its rather easy to see him.
Mu has to cancel his whole technique in order to use Jinton. His technique erases his chakra, he can't do other jutsu without revealing his chakra so he will have to completely reveal himself. Not to mention Sharingan sees and gives color to chakra, so spotting him is not difficult.
Even if Mu senses the build up and becomes invisible again, he wouldn't be able to evade it since he's too slow and he has nothing in his arsenal that can block LoS. He'd still get hit as Amaterasu would spawn where Itachi is looking, and that's where Mu is, whether he is visible or not.
If Mu goes invisible, clearly Itachi would put up a level 1 Susanoo to protect himself from any attack Mu might throw at him, as he won't be able to see or detect him.
And how do you know Onoki started prepping Jinton before him? He just sees Onoki up above.
Nagato was a sensor with knowledge on Amaterasu, and KA slowed Itachi down as it turned him from Kabuto's side to Naruto's side. That's not an accurate representation of Amaterasu's prep and fire speed.
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He was able to do much more than a Ribcage Susanoo and Amaterasu in the manga. I fail to see why he can't do less.
He doesn't need to close his eyes in order to prep Amaterasu. He can do it without doing so as shown in the scan above, so I do think that Amaterasu would be fired before Jinton.