I'd rejoice, as the ninja would finally start acting like ninja and stop acting like Saiyans.
Honestly, the only way I see everyone in IT getting their chakra back (Assuming it doesn't just immediately go back to them once Kaguya is killed/sealed/defeated) is if Naruto uses Ninshuu and equalizes all the chakra he has to everyone else. This still leave Sasuke having s06p chakra, so maybe he helps Naruto do it since Kishi wouldn't just let Sasuke keep his power if Naruto fodderizes himself for the sake of the SA
Other than that happening, people in the IT will come out as regular people.
I have a theory/prediction that I am working on that basically states this
-People in IT are normals now
-S06P will take back his chakra and all of the beasts chakra
-Naruto and Sasuke die sealing/killing Kaguya
-World goes on like nothing happened and those two fade into legend like S06P did.
Well can't they make it again.?????
lol
Chakra only exists in humans (not counting Ootsuki's and their children) because the sage gave people chakra through Ninshuu.
If all the chakra is taken, the only way to get chakra would be the God Tree, and that is debatable if it would exist after this arc