Madera stated that he died could be symbolic. Not only did his clan disagree with him, after he had used his brothers eyes also, but after the truce, no one was on his side, he risked all to defeat Shodamine and lost. Therefore many may have felt as he did that he was no longer a threat. In his mind he had no where to go, with no people so he was dead, he couldn't even communicate anymore with his brother. Also the bijuu effect... I believe at one point they simply roamed free, and as the shinobi world grew, seals, and ways of controlling them to keep them from specific areas were produced as well. With dominant clans like Senju and Uchiha, its easy to understand for example why the Sand sought out Shukaku and contained him within Gaara... simply to matter as a force. Without the assistance of a bijuu a clan would easily be attacked. Therefore this period is where Orochimaru got his ideas, but the Elders, and Hokages wanted full control of 'dangerous' things and never to be available to anyone withouth their permission. Lastly when the Kyuubi spoke to Sasuke inside of Naruto's head, he stated that Sasuke has the same murderous look in his eye as Madera, and the way he talked as if he had been an ally, thus battle vs. Shodamine. There was something sinister in the way the Kyuubi stated it, but he didn't say Madara sent me to Konoha, but also during that scene no one asked him.