what happened to madara is basically what was happening to obito when he first became a jin... The only difference is that Madara needed to be restrained and have his chakra absorbed for the transformation to happen successfully. Madara's still in there somewhere and he can still fight back. If he does begin to fight back, and succeeds, he could basically take control of the body and kick kaguya back into the sidelines. Kaguya's only been around for 1 chapter, and took out madara without him getting a chance to flash back or anything. I'm fairly certain madara's not done yet...
In any case, I'm pretty sure Kaguya's going to be boring as hell. The only useful thing about kaguya, right now, is the history lesson she may reveal to us... Really, what can kaguya do...? madara already slaughtered 3 hokage, gokage, Kakashi, guy, obito, the 9 bijuu, naruto and sasuke, 90% of SA, and literally succeeded in his plan of casting IT. What is kaguya going to bring to the table at this point...? Even obito severely ***** slapped naruto and sasuke, humiliated 3 of the hokage, kakashi, guy and bee, killed a shitload of SA, and nearly succeeded in his end goal. Unless kaguya kills everyone and the show just ends, she can't top what obito has done, let alone madara. I'm interested to see what kishi's going to do, with kaguya, at this point, but I have very low expectations considering how he handled madara and obito with all the power they had.