The most simple solution to how Madara was able to avoid dissipating after Kabuto was defeated is that Kabuto was not the one to use Edo Tensi on Madara.
Consider that Madara planned to come back from the dead long before Kabuto was even a player on the map.
Wouldn't it make sense that someone else knows Edo Tensi (Obito, perhaps taught by Madara or even Oro) and he used it to bring Madara back (coincidentally) at the same time Kabuto raised his army? I think Madara would have planned for the simplest revival
(via Obito), rather than going out on a limb and hoping someone random (Kabuto) would revive him sometime in the course of the war...
This poses the question can sharingan copy Edo Tensi?
Anyway, thats my theory.
If it is true, then killing Obito would also kill Madara. And then all we have to worry about is the rouge Juubi...