Of course he could. Kaguya is the Juubi, and Kakashi was going to Kamui the Juubi.
You must be registered for see images
He had chakra from Naruto, Kakashi already stated that he couldn't warp large objects on his own and that was when he warped 8 tails Bee and couldn't even warp the whole thing, he left a tentacle behind. Kaguya more than likely would sense it, escape into her own dimension, exist behind him and kill him with the ash bone.
She wouldn't let that happen, she might transport them to another dimension as she did with Kakashi, Sakura, Obito, Naruto, and Sasuke to the lava world which would have Kakashi falling to his death unless he warps himself away but he can't warp back or else he would be falling in lava again. Kamui works on what Kakashi have his vision on, she can shot needles at him which would distract him and would take up his sight of her. Plus Obito said he couldn't Kamui as Juubito because he was the Juubi Jin so I doubt Kakashi can warp her either way. Kinda sad that Madara was able to warp himself with Kamui, could be because he allowed Sasuke to cut him in halve, could be that Madara's master of the Sharingan in general allowed him to, could just be a huge plot hole, or Madara's power was greater.
You must be registered for see links