As for what you are all saying I can partially agree. We have been shown that other ninjas can gain control of and over power the bijuus.
I can not say that there is absolute truth that the Mangekyou Sharingan can control the Kyuubi. We know Madara had the power to control the Kyuubi and we did see the Kyuubi's power get suppressed by Sasuke, but I don't know if the MS can control the Kyuubi or at least not just any MS. Sasuke successfully suppressed a small portion of the Kyuubi's power and Jiraiya had also devised a seal to suppress a small portion of the Kyuubi's power. It is possible to suppress the Kyuubi's power, but not to fully control it. It has been emphasized time and time again that the Kyuubi's power is immense. Minato Namikaze had to summon a death god in order to just seal the Kyuubi away. I don't think it is possible for anyone in the manga excluding Madara to control the Kyuubi.
Since Madara is still a complete mystery one can not know how exactly he controlled the Kyuubi. Madara has been alive for so long so we don't know what secrets he found out. His EMS may not be responsible for controlling the Kyuubi.
I don't think Naruto will be a willing villain, but I do think that he will at least be responsible for much destruction. Naruto has shown time and time again that he has no desire to control the Kyuubi's power. By learning the Sage Mode Naruto has again rejected the opportunity to control the Kyuubi. People can say that the new powers Naruto has can help control the Kyuubi, but nature can not surpass an unstoppable force of destruction that is made of pure chakra. Naruto sees the Kyuubi's chakra as a curse and learning Sage Mode has just removed any chance of Naruto wanting to control the Kyuubi's chakra now that he has his own power. Even if the Kyuubi's power is a curse Naruto has to realize that he has to control that curse.
I also believe that Naruto may overcome the Kyuubi in the end, but it would be impossible for them to work together like Killerbee and Hachibi. Like I said above Naruto does not want to work with the Kyuubi. When the Kyuubi rejected Fukasaku-sama Naruto did not try to compromise with the Kyuubi at least to our knowledge. Instead he sought another method. Naruto wants to deny that the Kyuubi is in him and that will be his downfall.
In regards to Pein being a hero I do believe that he will be one. He won't be the hero like Naruto is, but he may accomplish something that will help save the world in the future. A power like the Rinnegan is too important in the story for a simple psychotic villain to use. Pein believes he is doing the right thing and the fact that he was one of Jiraiya's students emphasizes his importance. I believe with every fiber of my being that either Pein or his Rinnegan will make a positive difference in the story.