We don't really know exactly what he views as "the antiquated system that needs to be extinguished". Is it the power balance of bijuus stretched over the countries restraining each other? Or could it be the bijuus potential of making people bring them all together to create the Juubi and take control of the world? Is it the shinobi villages using the bijuus for war that is the problem?
Whether it is necessary to kill the Kyuubi or not, depends on what he sees as the antiquated system and what he needs to do in order to destroy it.
I think he just generally views the bijuu as a reason for all the bad things that have happened and feels like the world will be better off without them. I mean he does have a point in a way.