Will the Sharingan be able to subdue Naruto now that he has control over the chakra?
Right now it shouldn't. The sharingan is supposed to manipulate the mind part of the bijuu, not the chakra part. The mind part is sealed inside Naruto after it was defeated, so it takes no active role and cannot be manipulated, since it does not have any strength, and the chakra part is now Naruto's to control.
Do you think the Sharingan would be able to control that now and why yes/no?