1) He could have Kamui sniped that massive hand away. (Pew pew)
2) He could have Kamui'd behind her, grabbed her then kamui'd both himself and her to the dimension and come back next to Naruto and Sasuke.
3) He could have Kamui'd in front, used complete susano'o (not winged or perfect) and use a default spirit weapon to slice the arm.
4) Simply kamui her away from a long distance.
Kamui is so versatile and OP that I don't think Kakashi would ever have needed to use PS in the present or the future in an encounter. Unless of course he needed to fly, which could be Sasuke's role or even Naruto's role with his float tech.
Kishi has basically sparked a lot of claims about plot holes, ass pulls or illogicalness concerning his writing and Kakashi. Also Sasuke who is INDRA's reincarnation has basically had his susano'o stolen, rendering him quite ununique in regards to his SO6P power up and reincarnate status. Imagine Kaguya using Ashura bijuu mode? It would shit on Naruto who is supposed to be his reincarnate and supposedly has that form to utilise later.